Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2489
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: 32167
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1812 original size:13 final size:13
Alignment explanation
Indices: 1794--1818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1784 CATAAAATGT
1794 TGTATCGATACAA
1 TGTATCGATACAA
1807 TGTATCGATACA
1 TGTATCGATACA
1819 TATTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1834 original size:32 final size:33
Alignment explanation
Indices: 1774--1839 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1764 TTCAACGATT
1774 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
** *
1807 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1839 T
1 T
1840 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1898 original size:13 final size:13
Alignment explanation
Indices: 1880--1904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1870 ATTACTCAAA
1880 TGTATCGATACAT
1 TGTATCGATACAT
1893 TGTATCGATACA
1 TGTATCGATACA
1905 CTGATCTTTG
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):
TGTATCGATACAT
Found at i:2006 original size:52 final size:52
Alignment explanation
Indices: 1913--2036 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
1903 CACTGATCTT
*
1913 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
1964 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
2016 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2037 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:9493 original size:22 final size:22
Alignment explanation
Indices: 9467--9522 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
9457 TTTTTCTTTG
9467 TTTCT-ATTTCTTCTCTCTTTTT
1 TTTCTCATTT-TTCTCTCTTTTT
* *
9489 TTTCTCCTTTTTTTCTCTTTTT
1 TTTCTCATTTTTCTCTCTTTTT
* *
9511 TTTTTCTTTTTT
1 TTTCTCATTTTT
9523 TTAGTTGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTCATTTTTCTCTCTTTTT
Found at i:9524 original size:11 final size:11
Alignment explanation
Indices: 9480--9524 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
9470 CTATTTCTTC
9480 TCTCTTTTTTT
1 TCTCTTTTTTT
*
9491 TCTCCTTTTTT
1 TCTCTTTTTTT
9502 TCTCTTTTTTT
1 TCTCTTTTTTT
*
9513 TTTCTTTTTTT
1 TCTCTTTTTTT
9524 T
1 T
9525 AGTTGAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTCTTTTTTT
Found at i:11410 original size:20 final size:21
Alignment explanation
Indices: 11385--11433 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
11375 GCACTCGTTA
11385 GATGAAAAGACATACTT-TTG
1 GATGAAAAGACATACTTGTTG
**
11405 GATGAAAAGATGTACTTGTTG
1 GATGAAAAGACATACTTGTTG
*
11426 GACGAAAA
1 GATGAAAA
11434 AAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (21 bp):
GATGAAAAGACATACTTGTTG
Found at i:14670 original size:3 final size:3
Alignment explanation
Indices: 14662--14724 Score: 51
Period size: 3 Copynumber: 20.7 Consensus size: 3
14652 CTTATTAATA
* *
14662 TCT TCT TCT GTCT TCT TC- TCT T-T TTT TCT TGTT TCT TCT TCTT TCT
1 TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TC-T TCT
14708 TCT TC- TCT TGCT TCT TC
1 TCT TCT TCT T-CT TCT TC
14725 AAATACTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
2 6 0.12
3 33 0.66
4 11 0.22
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:14683 original size:33 final size:34
Alignment explanation
Indices: 14641--14720 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
14631 ATTTTCTTTT
14641 TTCTTCTCTTGCTTAT-TAATATCTTCTTCTGTC
1 TTCTTCTCTTGCTTATCTAATATCTTCTTCTGTC
* * ** * *
14674 TTCTTCTCTT-TTTTTCTTGTTTCTTCTTCTTTC
1 TTCTTCTCTTGCTTATCTAATATCTTCTTCTGTC
14707 TTCTTCTCTTGCTT
1 TTCTTCTCTTGCTT
14721 CTTCAAATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 3 0.08
33 33 0.87
34 2 0.05
ACGTcount: A:0.05, C:0.25, G:0.05, T:0.65
Consensus pattern (34 bp):
TTCTTCTCTTGCTTATCTAATATCTTCTTCTGTC
Found at i:14723 original size:7 final size:6
Alignment explanation
Indices: 14662--14724 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 6
14652 CTTATTAATA
* *
14662 TCTTCT TCTGTCT TCTTC- TCTT-T TTTTCT TGTTTCT TCTTCTT TCTTCT
1 TCTTCT TCT-TCT TCTTCT TCTTCT TCTTCT T-CTTCT TCTTC-T TCTTCT
14711 TC-TCT TGCTTCT TC
1 TCTTCT T-CTTCT TC
14725 AAATACTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
5 11 0.23
6 15 0.31
7 22 0.46
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.67
Consensus pattern (6 bp):
TCTTCT
Found at i:17009 original size:20 final size:20
Alignment explanation
Indices: 16984--17037 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
16974 CTACCACTGT
* *
16984 TTGTATCGATACATGGTCCA
1 TTGTATCGATACATGATCAA
*
17004 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
17024 TTGTATCGATACAT
1 TTGTATCGATACAT
17038 TGCTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:19284 original size:21 final size:20
Alignment explanation
Indices: 19250--19292 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
19240 TATTAAAAAG
*
19250 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
19271 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
19291 TT
1 TT
19293 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:19291 original size:20 final size:21
Alignment explanation
Indices: 19250--19292 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
19240 TATTAAAAAG
*
19250 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
19271 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
19291 TT
1 TT
19293 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:21642 original size:33 final size:34
Alignment explanation
Indices: 21579--21644 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
21569 TATTACAAGC
*
21579 AATGTATCGATACAATTTCATCATGTATCGATAT
1 AATGTATCGATACAATTTCACCATGTATCGATAT
21613 AATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 AATGTATCGATACAATT-TCACCATGTATCGATA
21645 CAAATAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (34 bp):
AATGTATCGATACAATTTCACCATGTATCGATAT
Found at i:24252 original size:13 final size:13
Alignment explanation
Indices: 24233--24274 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
24223 AAATAGTACC
24233 CAATGTATCGATA
1 CAATGTATCGATA
* *
24246 TAATGTATTGATA
1 CAATGTATCGATA
*
24259 CATTGTATCGATA
1 CAATGTATCGATA
24272 CAA
1 CAA
24275 GGAATGTTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:28818 original size:3 final size:3
Alignment explanation
Indices: 28810--28834 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28800 TCCGAGTCAC
28810 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
28835 TTCCTCTTCA
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:29773 original size:13 final size:13
Alignment explanation
Indices: 29755--29811 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
29745 CATAAAGTGT
29755 TGTATCGATACAA
1 TGTATCGATACAA
29768 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
29783 GTGTTGTACCGATACAA
1 ----TGTATCGATACAA
29800 TGTATCGATACA
1 TGTATCGATACA
29812 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:29790 original size:32 final size:32
Alignment explanation
Indices: 29737--29832 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
29727 CAATGATTTA
29737 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
29770 TATCGATACATAAGTGTTGTACCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
29802 TATCGATACATAAGTTTTGTATCGATACAAT
1 TATCGATACATAAGTGTTGTATCGATACAAT
29833 TTAAGCTACT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.82
33 11 0.18
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:29824 original size:19 final size:18
Alignment explanation
Indices: 29737--29830 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
29727 CAATGATTTA
29737 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
29757 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
29770 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
*
29789 TACCGATAC--AA---TG
1 TATCGATACATAAGTTTG
29802 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
29821 TATCGATACA
1 TATCGATACA
29831 ATTTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:29891 original size:13 final size:13
Alignment explanation
Indices: 29873--29897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29863 ATTACTCAAA
29873 TGTATCGATACAT
1 TGTATCGATACAT
29886 TGTATCGATACA
1 TGTATCGATACA
29898 CTGATCTTTG
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):
TGTATCGATACAT
Found at i:29950 original size:52 final size:51
Alignment explanation
Indices: 29886--30034 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
29876 ATCGATACAT
**
29886 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
29938 TGTATCGATACACTA-CAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATC--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
29990 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTT
30035 TCATATTTCG
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 86 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Done.