Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1434
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: 40615
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7967 original size:27 final size:27
Alignment explanation
Indices: 7937--8114 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
7927 ATATTGAGTC
* * * *
7937 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
7964 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
7991 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
8019 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
8046 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
8073 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
8100 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8115 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:8076 original size:82 final size:81
Alignment explanation
Indices: 7958--8113 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
7948 TGCTATATAA
* *
7958 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
8023 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
8040 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
8104 CACTTAGTGC
65 CACTTAGTGC
8114 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:13723 original size:14 final size:13
Alignment explanation
Indices: 13693--13727 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
13683 TTCATGCATG
13693 TTTT-TTTTATTT
1 TTTTATTTTATTT
13705 TTTTATTTTATTT
1 TTTTATTTTATTT
13718 TATTTATTTT
1 T-TTTATTTT
13728 TTAGCTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 9 0.43
14 8 0.38
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:14951 original size:39 final size:40
Alignment explanation
Indices: 14871--14967 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
14861 TGGATGATAA
* *
14871 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAACTATAT
*
14911 CCGGGCTATGTCCCGAAGGCATT-GAGCGAGTAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAACTATAT
* *
14950 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
14968 TACTTGGCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 13 0.25
39 16 0.31
40 22 0.43
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAACTATAT
Found at i:28232 original size:47 final size:47
Alignment explanation
Indices: 28163--28291 Score: 231
Period size: 47 Copynumber: 2.7 Consensus size: 47
28153 TCAATGGATA
*
28163 AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTTATCCTGG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCTGG
*
28210 AGTACCTATACAATGGCCCGTAGCCAAATCAAGGTAACTTATCCTGG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCTGG
*
28257 AGTACCTATACCATGGCCTGTAGCCAAATCAAGGT
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGT
28292 TTAACTCACA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 78 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCTGG
Found at i:29625 original size:46 final size:46
Alignment explanation
Indices: 29575--29744 Score: 184
Period size: 46 Copynumber: 3.7 Consensus size: 46
29565 TTGAGCATGT
* *
29575 GAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * * *
29621 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCC
* *
29668 GAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * *
29714 GAGCTCATTGAGTTGAGTTCGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29745 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 55 0.54
47 29 0.28
48 3 0.03
50 6 0.06
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:30006 original size:19 final size:20
Alignment explanation
Indices: 29969--30006 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29959 ATAAGCTGGT
29969 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
29989 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
30007 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:37153 original size:45 final size:46
Alignment explanation
Indices: 37104--37272 Score: 188
Period size: 45 Copynumber: 3.7 Consensus size: 46
37094 TGGTTGAGCA
*
37104 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG-
1 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * *
37149 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGC
*
37194 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC-AACGC
1 -T-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* *
37241 CCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTA
1 TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
37273 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
42 6 0.06
44 15 0.14
45 46 0.44
46 1 0.01
47 30 0.29
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:37532 original size:19 final size:20
Alignment explanation
Indices: 37495--37532 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
37485 ATAAGGTGGT
37495 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
37515 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
37533 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Done.