Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2610
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: 19129
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:2265 original size:3 final size:3
Alignment explanation
Indices: 2257--2291 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2247 ACATAAAATC
2257 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2292 TGACTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2398 original size:47 final size:47
Alignment explanation
Indices: 2328--2420 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
2318 CTACTCCTGA
*
2328 AGAGTCGGTTTATTCGTTCAGTTTTATTGCCAAATCTTGAACCTAATG
1 AGAGTCGGTTTATTCGATCAGTTTTATTG-CAAATCTTGAACCTAATG
2376 AGAGTC-GTTTATTCGATCAGTTTTATTGCAAATCTTGAACCTAAT
1 AGAGTCGGTTTATTCGATCAGTTTTATTGCAAATCTTGAACCTAAT
2421 TACCAATTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 17 0.39
47 21 0.48
48 6 0.14
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (47 bp):
AGAGTCGGTTTATTCGATCAGTTTTATTGCAAATCTTGAACCTAATG
Found at i:3062 original size:2 final size:2
Alignment explanation
Indices: 3055--3099 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3045 GCGCTCCATT
3055 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3096 TA TA
1 TA TA
3100 AAGTCACTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12957 original size:28 final size:27
Alignment explanation
Indices: 12887--12962 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
12877 TTTCTTCACA
*
12887 ATCGGGGACACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
12914 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
12940 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
12963 ACTTTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.50
28 18 0.41
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:13007 original size:51 final size:50
Alignment explanation
Indices: 12945--13114 Score: 160
Period size: 52 Copynumber: 3.3 Consensus size: 50
12935 TTATTTTCGA
**
12945 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGA-TTTATTTTCAAAATATCAATTTTTCATAATC
* * * * * *
12996 GGGGATACTCCAACCCCGGTTTTAATTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCC-GATTTATTTTCAAAATATCAATTTTTC-ATAATC
** * * *
13048 GGGGATACTCCAACATCGATTCTATTTCCAAAAATATCAATTTTTCACAATT
1 GGGGATACTCCAACCCCGATT-TATTTTC-AAAATATCAATTTTTCATAATC
**
13100 AAGGATACTCCAACC
1 GGGGATACTCCAACC
13115 TCGTCAATTC
Statistics
Matches: 93, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
51 39 0.42
52 41 0.44
53 13 0.14
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTATTTTCAAAATATCAATTTTTCATAATC
Found at i:13145 original size:211 final size:211
Alignment explanation
Indices: 12781--13173 Score: 558
Period size: 211 Copynumber: 1.9 Consensus size: 211
12771 AATTCTCCAC
* * * * *
12781 AATCGGGGATATTCCAACTCCGATTTTATTTTTAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTAATTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* ** *
12846 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTCA
* * * *
12911 ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTTTCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTTCAA
12976 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
* *
12992 AATCGGGGATACTCCAACCCCGGTTTTAATTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTAATTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* * * * *
13057 CCAACAT-CGATTCTATTTCC-AAAAATATCAATTT-TTCACAATTAAGGATACTCCAACCTCGT
65 CCAAC-TCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGT
13119 CAATTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
129 CAA-TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
13174 TTATTATCTC
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
210 25 0.16
211 100 0.63
212 33 0.21
213 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGATTTTAATTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCAAGGACACTCCAACCCCGTCA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTTCAA
AATATTGATTTTTCAT
Found at i:14494 original size:51 final size:51
Alignment explanation
Indices: 14438--14539 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
14428 TGTACAATAT
*
14438 GTACATAATTAAAGCATTATTAATGTACAAATTTACTACATAAATATTTTA
1 GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
14489 GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
1 GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
14540 TTACTATTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (51 bp):
GTACATAATTAAAGCATTATGAATGTACAAATTTACTACATAAATATTTTA
Found at i:15339 original size:20 final size:20
Alignment explanation
Indices: 15311--15385 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
15301 TCATACCCTG
15311 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
15331 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
15351 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
15371 ATGTATCGATACATT
1 ATGTATCGATACATT
15386 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:15378 original size:40 final size:39
Alignment explanation
Indices: 15311--15388 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
15301 TCATACCCTG
* *
15311 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
15351 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
15389 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:17133 original size:130 final size:130
Alignment explanation
Indices: 16900--17160 Score: 522
Period size: 130 Copynumber: 2.0 Consensus size: 130
16890 ATTTTCTTAG
16900 TATTTTTCCTGTGAAGTATGTCAAAATACCTTTCCAATGGTGTCTTATTTGCCCCTGGATCATTA
1 TATTTTTCCTGTGAAGTATGTCAAAATACCTTTCCAATGGTGTCTTATTTGCCCCTGGATCATTA
16965 CGTATGATAGAGTTATGATTTTTTGAACCCAAACTGTCCAGAACCCATGGAATCAGCGATTCGCA
66 CGTATGATAGAGTTATGATTTTTTGAACCCAAACTGTCCAGAACCCATGGAATCAGCGATTCGCA
17030 TATTTTTCCTGTGAAGTATGTCAAAATACCTTTCCAATGGTGTCTTATTTGCCCCTGGATCATTA
1 TATTTTTCCTGTGAAGTATGTCAAAATACCTTTCCAATGGTGTCTTATTTGCCCCTGGATCATTA
17095 CGTATGATAGAGTTATGATTTTTTGAACCCAAACTGTCCAGAACCCATGGAATCAGCGATTCGCA
66 CGTATGATAGAGTTATGATTTTTTGAACCCAAACTGTCCAGAACCCATGGAATCAGCGATTCGCA
17160 T
1 T
17161 TCTGGTCGGG
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (130 bp):
TATTTTTCCTGTGAAGTATGTCAAAATACCTTTCCAATGGTGTCTTATTTGCCCCTGGATCATTA
CGTATGATAGAGTTATGATTTTTTGAACCCAAACTGTCCAGAACCCATGGAATCAGCGATTCGCA
Done.