Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold902
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: 21051
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Found at i:2271 original size:51 final size:51
Alignment explanation
Indices: 2197--2417 Score: 207
Period size: 52 Copynumber: 4.3 Consensus size: 51
2187 TTAATCATCG
* * *** *
2197 GGGATACTCCAACCCCGACTTTATTTTC-AAAATATTGATTTTTCATAATC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTTCACAATC
* * * *
2247 AGGGATACTCCAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCGCAATC
1 -GGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTT-CACAATC
* **
2299 GGGGATACTCCAACCCC-AGTTTTATTTTC-AAAACACCAATTTTCCTTTAATC
1 -GGGATACTCCAACCCCGA-TTTTATTTTCAAAAACACCAATTTTTC-ACAATC
* * *
2351 GAGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 G-GGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTTCACAATC
2403 GAGGATACTCCAACC
1 G-GGATACTCCAACC
2418 TCGTTATTTC
Statistics
Matches: 142, Mismatches: 20, Indels: 15
0.80 0.11 0.08
Matches are distributed among these distances:
50 3 0.02
51 37 0.26
52 84 0.59
53 18 0.13
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTTCACAATC
Found at i:2409 original size:104 final size:103
Alignment explanation
Indices: 2193--2417 Score: 267
Period size: 104 Copynumber: 2.2 Consensus size: 103
2183 CCCGTTAATC
* *** *
2193 ATCGGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATCAGGGATACTCC
1 ATCGGGGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTCCATAATCAGGGATACTCC
* * * *
2258 AACCCCGATTTTATTGCTAAAACACTAATTTTTCCGCA
66 AACCCCGATTTTATTCCAAAAACACCAATTTTTCCACA
* *
2296 ATCGGGGATACTCCAACCCC-AGTTTTATTTTCAAAACACCAATTTTCCTTTAATC-GAGGATAC
1 ATCGGGGATACTCCAACCCCGA-CTTTATTTTCAAAACACCAATTTTCC-ATAATCAG-GGATAC
* *
2359 TCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACA
63 TCCAACCCCGATTTTA-TTCCAAAAACACCAATTTTTCCACA
*
2400 ATCGAGGATACTCCAACC
1 ATCGGGGATACTCCAACC
2418 TCGTTATTTC
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
102 1 0.01
103 41 0.39
104 46 0.44
105 16 0.15
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (103 bp):
ATCGGGGATACTCCAACCCCGACTTTATTTTCAAAACACCAATTTTCCATAATCAGGGATACTCC
AACCCCGATTTTATTCCAAAAACACCAATTTTTCCACA
Found at i:2436 original size:28 final size:28
Alignment explanation
Indices: 2400--2476 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2390 ATTTTTCACA
* * *
2400 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2428 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2456 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2477 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2550 original size:28 final size:29
Alignment explanation
Indices: 2510--2564 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2500 TCTCATAATT
*
2510 GGGGATACTCCAA-CCCCGTTATTTTTGA
1 GGGGATACTCCAATCCCCATTATTTTTGA
*
2538 GGGGATACTCCAATCCCCATTTTTTTT
1 GGGGATACTCCAATCCCCATTATTTTT
2565 CTAATCATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (29 bp):
GGGGATACTCCAATCCCCATTATTTTTGA
Found at i:4699 original size:4 final size:4
Alignment explanation
Indices: 4692--4716 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4682 TCTTGAGGTG
4692 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
4717 ATATCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:8890 original size:21 final size:21
Alignment explanation
Indices: 8866--8905 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8856 AACATGTCAT
8866 AATGCATGAAGCATAGCTTAA
1 AATGCATGAAGCATAGCTTAA
* *
8887 AATGCATGAATCATGGCTT
1 AATGCATGAAGCATAGCTT
8906 GTTAACATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (21 bp):
AATGCATGAAGCATAGCTTAA
Found at i:9845 original size:52 final size:51
Alignment explanation
Indices: 9760--9883 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
9750 ATATGAAAAG
* *
9760 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
9811 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
9863 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
9884 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:9896 original size:51 final size:51
Alignment explanation
Indices: 9760--9903 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
9750 ATATGAAAAG
*
9760 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
9812 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
9863 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
9904 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:9910 original size:13 final size:13
Alignment explanation
Indices: 9892--9916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9882 CAAAGATCAG
9892 TGTATCGATACAA
1 TGTATCGATACAA
9905 TGTATCGATACA
1 TGTATCGATACA
9917 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:9997 original size:13 final size:13
Alignment explanation
Indices: 9979--10003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9969 CAAAAAAATA
9979 TGTATCGATACAT
1 TGTATCGATACAT
9992 TGTATCGATACA
1 TGTATCGATACA
10004 ACATTTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10018 original size:33 final size:33
Alignment explanation
Indices: 9957--10023 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
9947 AGTAGCTTAA
*
9957 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATATATCGATAC
* ***
9990 ATTGTATCGATACAACATTTTATATATCGATAC
1 ATTGTATCGATACAAAAAAATATATATCGATAC
10023 A
1 A
10024 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATATATCGATAC
Found at i:11054 original size:91 final size:93
Alignment explanation
Indices: 10882--11061 Score: 285
Period size: 91 Copynumber: 1.9 Consensus size: 93
10872 AAAAGGATGT
10882 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTGATT
*
10947 CAAGGCCAGCTATATTGGACTTAAGGTGC
65 CAAGGCCAGCGATATTGGACTTAAGGTGC
* *
10976 CAATGTGCTGATTCAAGGTC-AGCTACATTGGACTTAAATAT-G-AAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGG-CGAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATT
*
11038 TAAGGCCAGCGATATTGGACTTAA
65 CAAGGCCAGCGATATTGGACTTAA
11062 AGGCAAGGTG
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.52
93 1 0.01
94 37 0.46
95 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (93 bp):
CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAGGTGC
Found at i:11055 original size:49 final size:49
Alignment explanation
Indices: 10969--11113 Score: 195
Period size: 49 Copynumber: 3.0 Consensus size: 49
10959 TATTGGACTT
* * * *
10969 AAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATG-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-AGGC
* *
11018 AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT-AAAGGC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
* *
11066 AAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGGCTTAAAAGG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGG
11114 AGACGCCACC
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 2 0.02
48 40 0.48
49 42 0.50
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (49 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAGGC
Found at i:11091 original size:48 final size:46
Alignment explanation
Indices: 10882--11110 Score: 232
Period size: 48 Copynumber: 4.8 Consensus size: 46
10872 AAAAGGATGT
* * * *
10882 CAATGTGCTGATTCAAGGCGAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G--AAGGTGC
10934 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
* * *
10976 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GAAGGTGC
* *
11025 CAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G-AAGGTGC
* *
11073 CAATATGCTAATTCAAGGCCAGCTATATTGGGCTTAAA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
11111 AGGAGACGCC
Statistics
Matches: 152, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
42 39 0.26
47 2 0.01
48 43 0.28
49 37 0.24
52 31 0.20
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (46 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGGTGC
Found at i:11213 original size:30 final size:30
Alignment explanation
Indices: 11154--11258 Score: 178
Period size: 30 Copynumber: 3.6 Consensus size: 30
11144 AGGTTTGCAT
* *
11154 CACTGACTTGTGGGCTTTT--AAAGGTTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
11182 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
11212 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAAGGGTGC
11242 CACTAACTTGTGGGCTT
1 CACTAACTTGTGGGCTT
11259 AAAAAGAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
28 18 0.25
30 55 0.75
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (30 bp):
CACTAACTTGTGGGCTTTTGAAAAGGGTGC
Found at i:11367 original size:27 final size:28
Alignment explanation
Indices: 11329--11390 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
11319 CTTCGAAAAA
* *
11329 AAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAGGGTGCCACTGACTTGTGGACTTTTG
*
11356 AAGGTTGCCACTGACTTGTGGACTTTTG
1 AAGGGTGCCACTGACTTGTGGACTTTTG
11384 AAGGGTG
1 AAGGGTG
11391 ATAAATGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (28 bp):
AAGGGTGCCACTGACTTGTGGACTTTTG
Found at i:12826 original size:1 final size:1
Alignment explanation
Indices: 12820--12921 Score: 78
Period size: 1 Copynumber: 102.0 Consensus size: 1
12810 ATCCAGACCC
* * * ** * * ** *
12820 TTTTTTTTTTGTTTTTTTTTTTGTTTTTTTCTTTGGTATTTTTGTTTTTGCTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
12885 GTTTTTTTTGTTTTGTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12922 GTGAGGACGC
Statistics
Matches: 76, Mismatches: 25, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (1 bp):
T
Found at i:12839 original size:14 final size:14
Alignment explanation
Indices: 12820--12921 Score: 104
Period size: 15 Copynumber: 7.4 Consensus size: 14
12810 ATCCAGACCC
12820 TTTTTTTTTTG--T
1 TTTTTTTTTTGTTT
12832 TTTTTTTTTTG-TT
1 TTTTTTTTTTGTTT
* * *
12845 TTTTTCTTTGGTAT
1 TTTTTTTTTTGTTT
*
12859 TTTTGTTTTTGCTTT
1 TTTTTTTTTTG-TTT
12874 TTTTTTGTTTTGTTT
1 TTTTTT-TTTTGTTT
*
12889 TTTTTGTTTTGTTT
1 TTTTTTTTTTGTTT
12903 GTTTTTTTTTT-TTT
1 -TTTTTTTTTTGTTT
12917 TTTTT
1 TTTTT
12922 GTGAGGACGC
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
12 11 0.15
13 15 0.20
14 20 0.27
15 24 0.32
16 5 0.07
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Done.