Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3297
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: 19324
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Found at i:5465 original size:39 final size:39
Alignment explanation
Indices: 5288--5454 Score: 271
Period size: 39 Copynumber: 4.3 Consensus size: 39
5278 CGAGACTTTA
*
5288 AGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
5327 AGTCCGGATATAACGCCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
* *
5366 AGCCCGGATATAGCACCAGCACGAATGCCTTCAGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
5405 AGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
*
5444 AGCCCAGATAT
1 AGCCCGGATAT
5455 TTTTCCAGCA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 117 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:5490 original size:78 final size:78
Alignment explanation
Indices: 5288--5571 Score: 258
Period size: 78 Copynumber: 3.6 Consensus size: 78
5278 CGAGACTTTA
* * * * **
5288 AGCCCGGATATAATACCAGCACGAATGCCTTCGGGAC-TT-AGTCCGGATATAACGCCAGCACGA
1 AGCCCGGATATATTTCCAGCACTAA-GCCTGC-GGACTTTAAGTCCGGATATAATACCAGCACGA
5351 ATGCCTTCGGGACTT
64 ATGCCTTCGGGACTT
*** * * *
5366 AGCCCGGATATAGCACCAGCACGAATGCCTTCAGGAC-TT-AGCCCGGATATAATACCAGCACGA
1 AGCCCGGATATATTTCCAGCACTAA-GCCTGC-GGACTTTAAGTCCGGATATAATACCAGCACGA
5429 ATGCCTTCGGGACTT
64 ATGCCTTCGGGACTT
* * * * * * *
5444 AGCCCAGATATTTTTCCAGCACTTAGCCTGCGGACTTTAAGTCCGGATATATTTCCAGCA-TAAA
1 AGCCCGGATATATTTCCAGCACTAAGCCTGCGGACTTTAAGTCCGGATATAATACCAGCACGAAT
*
5508 GCCTGC-GGACTT
66 GCCTTCGGGACTT
* *
5520 CAAGTCCGGATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGTCCGGATAT
1 --AGCCCGGATATATTTCCAGCACT-AAGCCTGCGGACTTTAAGTCCGGATAT
5572 TTTTCCAATA
Statistics
Matches: 176, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
76 10 0.06
77 15 0.09
78 151 0.86
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (78 bp):
AGCCCGGATATATTTCCAGCACTAAGCCTGCGGACTTTAAGTCCGGATATAATACCAGCACGAAT
GCCTTCGGGACTT
Found at i:5493 original size:39 final size:39
Alignment explanation
Indices: 5450--5578 Score: 206
Period size: 39 Copynumber: 3.3 Consensus size: 39
5440 ACTTAGCCCA
* * *
5450 GATATTTTTCCAGCACT-TAGCCTGCGGACTTTAAGTCCG
1 GATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGTCCG
5489 GATATATTTCCAGCATAAAGCCTGCGGACTTCAAGTCCG
1 GATATATTTCCAGCATAAAGCCTGCGGACTTCAAGTCCG
5528 GATATATTTCCAGCATAAAGCCTGCGGACTTCAAGTCCG
1 GATATATTTCCAGCATAAAGCCTGCGGACTTCAAGTCCG
*
5567 GATATTTTTCCA
1 GATATATTTCCA
5579 ATACCATGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
38 1 0.01
39 84 0.99
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (39 bp):
GATATATTTCCAGCATAAAGCCTGCGGACTTCAAGTCCG
Found at i:7943 original size:27 final size:27
Alignment explanation
Indices: 7913--8090 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
7903 ATATTGAGTC
** * *
7913 CGCACACGCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
7940 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
7967 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
7995 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
8022 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
8049 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
8076 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8091 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:8004 original size:55 final size:55
Alignment explanation
Indices: 7913--8090 Score: 202
Period size: 54 Copynumber: 3.3 Consensus size: 55
7903 ATATTGAGTC
** * * *
7913 CGCACACGCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
7967 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATAGTC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
8022 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATCATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
8076 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
8091 GTACAATTTA
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:8052 original size:82 final size:81
Alignment explanation
Indices: 7934--8089 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
7924 TGCTATACAA
* *
7934 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
7999 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
8016 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
8080 CACTTAGTGC
65 CACTTAGTGC
8090 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:15997 original size:27 final size:27
Alignment explanation
Indices: 15967--16144 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15957 ATATTGAGTC
* * * *
15967 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
15994 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16021 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16049 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16076 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16103 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16130 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16145 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:16106 original size:82 final size:81
Alignment explanation
Indices: 15988--16143 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
15978 TGCTATATAA
* *
15988 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16053 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16070 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16134 CACTTAGTGC
65 CACTTAGTGC
16144 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
Done.