Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1197
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: 31972
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:186 original size:3 final size:3
Alignment explanation
Indices: 178--202 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
168 AACCATGTTC
178 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
203 TTGATTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:4378 original size:13 final size:13
Alignment explanation
Indices: 4360--4385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4350 ACATTTCTTT
4360 ATGTATCGATACA
1 ATGTATCGATACA
4373 ATGTATCGATACA
1 ATGTATCGATACA
4386 TTGTCCCATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4397 original size:33 final size:33
Alignment explanation
Indices: 4341--4405 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
4331 TTGGGCATAT
**
4341 TGTATCGATACATTTCTTTATGTATCGATACAA
1 TGTATCGATACATTTCTCCATGTATCGATACAA
*
4374 TGTATCGATACATTGTC-CCATGTATTGATACA
1 TGTATCGATACATT-TCTCCATGTATCGATACA
4406 TTTCATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATTTCTCCATGTATCGATACAA
Found at i:8753 original size:20 final size:19
Alignment explanation
Indices: 8728--8783 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
8718 TTGGGCATAT
*
8728 TGTATCGATACATTTCTTCA
1 TGTATCGATACATTTC-CCA
*
8748 TGTATCGATGCATTGTCCCA
1 TGTATCGATACATT-TCCCA
*
8768 TGTATTGATACATTTC
1 TGTATCGATACATTTC
8784 ACTTAGGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTTCCCA
Found at i:8853 original size:19 final size:19
Alignment explanation
Indices: 8808--8863 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
8798 CTACCACTTT
*
8808 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
8828 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
8847 CATGTATCGATACAATG
1 CATGTATCGATACAATG
8864 TATCAATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:13369 original size:22 final size:22
Alignment explanation
Indices: 13342--13383 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13332 ATCAAAATAT
13342 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
* *
13364 ATTTCTCCTCCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
13384 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:21487 original size:13 final size:13
Alignment explanation
Indices: 21469--21499 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
21459 ACAATTCATC
21469 ATGTATCGATACA
1 ATGTATCGATACA
21482 ATGTATCGATACA
1 ATGTATCGATACA
21495 ATGTA
1 ATGTA
21500 CCATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21487 original size:33 final size:33
Alignment explanation
Indices: 21447--21515 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
21437 CCGTTACAAG
* *
21447 CAATGTATTGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
21480 CAATGTATCGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
21513 CAA
1 CAA
21516 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:21607 original size:32 final size:32
Alignment explanation
Indices: 21566--21642 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
21556 CAATTATCCT
21566 TGTATCGATACAATGAATATGTATCAATCCAA
1 TGTATCGATACAATGAATATGTATCAATCCAA
21598 TGTATCGATACAATGAATATGTATCAATCCAA
1 TGTATCGATACAATGAATATGTATCAATCCAA
21630 TGTATCGATACAA
1 TGTATCGATACAA
21643 AGCATAATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAATGAATATGTATCAATCCAA
Found at i:21630 original size:19 final size:19
Alignment explanation
Indices: 21566--21631 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 19
21556 CAATTATCCT
* *
21566 TGTATCGATACAATGAATA
1 TGTATCAATCCAATGAATA
21585 TGTATCAATCCAATG--TA
1 TGTATCAATCCAATGAATA
21602 TCG-AT--A--CAATGAATA
1 T-GTATCAATCCAATGAATA
21617 TGTATCAATCCAATG
1 TGTATCAATCCAATG
21632 TATCGATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
13 5 0.14
14 1 0.03
15 6 0.16
17 6 0.16
18 1 0.03
19 18 0.49
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCAATCCAATGAATA
Found at i:22095 original size:13 final size:13
Alignment explanation
Indices: 22077--22101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22067 ATATTGCTTG
22077 GTATCGATACATT
1 GTATCGATACATT
22090 GTATCGATACAT
1 GTATCGATACAT
22102 GTTCTTTGTA
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):
GTATCGATACATT
Found at i:22098 original size:33 final size:32
Alignment explanation
Indices: 22056--22119 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
22046 CTGACCTAAA
22056 TGTATCGATACATATTGCTTGGTATCGATACAT
1 TGTATCGATACATATT-CTTGGTATCGATACAT
* *
22089 TGTATCGATACATGTTCTTTGTATCGATACA
1 TGTATCGATACATATTCTTGGTATCGATACA
22120 CCATAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATATTCTTGGTATCGATACAT
Found at i:23864 original size:3 final size:3
Alignment explanation
Indices: 23856--23911 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
23846 CCAAGAGGAA
*
23856 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
23904 GAT GAT GA
1 GAT GAT GA
23912 AAAGAAAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:30098 original size:35 final size:35
Alignment explanation
Indices: 30059--30129 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
30049 TCTGGAACCT
* * *
30059 TTTATGCGTTTAATGAATGAATTGTTTTTCTTACA
1 TTTATGCATTTAATAAAAGAATTGTTTTTCTTACA
30094 TTTATGCATTTAATAAAAGAATTGTTTTTCTTACA
1 TTTATGCATTTAATAAAAGAATTGTTTTTCTTACA
30129 T
1 T
30130 GCTTTGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (35 bp):
TTTATGCATTTAATAAAAGAATTGTTTTTCTTACA
Done.