Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold794
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: 47317
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:4211 original size:40 final size:40
Alignment explanation
Indices: 4156--4371 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
4146 CGGATGATAA
* *
4156 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
4196 CGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
4235 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
**
4275 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
4315 CGGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
4355 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
4372 TACTTGGTTT
Statistics
Matches: 164, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
39 53 0.32
40 110 0.67
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:4287 original size:79 final size:80
Alignment explanation
Indices: 4156--4371 Score: 298
Period size: 79 Copynumber: 2.7 Consensus size: 80
4146 CGGATGATAA
* *
4156 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCA-TTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTG
**
4219 TGCGAGTTACTA-ATTC
65 TGCGAACTACTATA-TC
4235 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
4300 GCGAACTACTATATC
66 GCGAACTACTATATC
* * * *
4315 CGGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
4372 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
79 72 0.58
80 52 0.42
81 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAACTACTATATC
Found at i:4367 original size:119 final size:119
Alignment explanation
Indices: 4156--4371 Score: 307
Period size: 119 Copynumber: 1.8 Consensus size: 119
4146 CGGATGATAA
* * *
4156 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTGTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCAACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTGAG
*
4221 CGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
66 CGAGTTACTAATTCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATATC
4275 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-AACTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATT-
*
4338 GAGCGAG-TAGCT-ATATCC-GGTTAAATCCCGAAGG
63 GAGCGAGTTA-CTAAT-TCCGGGCTAAATCCCGAAGG
4372 TACTTGGTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
118 2 0.02
119 72 0.83
120 13 0.15
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (119 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCAACTGACTAATTCCGGGCTAAGTCCCGAAGGCATTGAG
CGAGTTACTAATTCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:6207 original size:35 final size:35
Alignment explanation
Indices: 6166--6234 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
6156 AATTAAAAAC
*
6166 ATAAAATAATAAAATAAATATTTCTAAACATCTTT
1 ATAAAATAATAAAAGAAATATTTCTAAACATCTTT
6201 ATAAAATAATAAAAGAAATATTTCTAAACATCTT
1 ATAAAATAATAAAAGAAATATTTCTAAACATCTT
6235 CATCACTGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (35 bp):
ATAAAATAATAAAAGAAATATTTCTAAACATCTTT
Found at i:9694 original size:23 final size:23
Alignment explanation
Indices: 9664--9708 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9654 GGGAAGTGAT
*
9664 CTTTTCTTGTGGTGCCATTCAGC
1 CTTTTCTTGTGGCGCCATTCAGC
*
9687 CTTTTCTTGTGGCGTCATTCAG
1 CTTTTCTTGTGGCGCCATTCAG
9709 TTTCCTGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (23 bp):
CTTTTCTTGTGGCGCCATTCAGC
Found at i:12053 original size:39 final size:40
Alignment explanation
Indices: 11837--12043 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
11827 GGATTGATAC
* *
11837 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
**
11877 TTGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
11916 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
11956 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
11996 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
12036 CC-GGCTAA
1 CCGGGCTAA
12044 ACTCCGAAGG
Statistics
Matches: 154, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 41 0.27
40 113 0.73
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:19457 original size:7 final size:7
Alignment explanation
Indices: 19440--19478 Score: 55
Period size: 6 Copynumber: 5.7 Consensus size: 7
19430 TTCAAACTAC
19440 TTTTTATT
1 TTTTTA-T
19448 TTTTTAT
1 TTTTTAT
19455 TTTTTA-
1 TTTTTAT
19461 TTTTTA-
1 TTTTTAT
19467 TTTTTAT
1 TTTTTAT
19474 TTTTT
1 TTTTT
19479 TAGCAGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.40
7 12 0.40
8 6 0.20
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:21663 original size:13 final size:13
Alignment explanation
Indices: 21645--21670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21635 ATATTATAAT
21645 TATTTTATGTTAA
1 TATTTTATGTTAA
21658 TATTTTATGTTAA
1 TATTTTATGTTAA
21671 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:23095 original size:40 final size:40
Alignment explanation
Indices: 23047--23252 Score: 344
Period size: 40 Copynumber: 5.2 Consensus size: 40
23037 GGACTAAGAT
23047 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
23087 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
23127 CCGAAGGCATTTGTGCTAGTGACTATATCCAGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
23167 CCGAAGGCATCTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
23207 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
23246 CCGAAGG
1 CCGAAGG
23253 TACTTGGGTT
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 15 0.10
40 141 0.90
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:31411 original size:5 final size:5
Alignment explanation
Indices: 31401--31429 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31391 ATTAATAAAT
31401 AATTA AATTA AATTA AATTA AATTA AATT
1 AATTA AATTA AATTA AATTA AATTA AATT
31430 GCAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:38476 original size:46 final size:46
Alignment explanation
Indices: 38425--38600 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
38415 TGGTTGAGCA
38425 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
38471 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
38516 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
38564 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38601 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 62 0.56
47 29 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:38581 original size:93 final size:93
Alignment explanation
Indices: 38422--38592 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
38412 GGATGGTTGA
*
38422 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
38487 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
38515 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
38579 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
38593 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:46008 original size:46 final size:45
Alignment explanation
Indices: 45958--46132 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
45948 TGGTTGAGCA
45958 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
46004 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
46050 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
46096 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46133 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 4 0.04
46 96 0.87
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:46112 original size:92 final size:92
Alignment explanation
Indices: 45955--46125 Score: 308
Period size: 92 Copynumber: 1.9 Consensus size: 92
45945 GGATGGTTGA
*
45955 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
46020 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
*
46047 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
46111 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
46126 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 2 0.03
92 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Done.