Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5354.1
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: 25626
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.30
Warning! 638 characters in sequence are not A, C, G, or T
Found at i:2002 original size:19 final size:20
Alignment explanation
Indices: 1965--2002 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1955 AACATTTTTG
*
1965 ATTCAACTTATTCGAGCTCA
1 ATTCAACTCATTCGAGCTCA
1985 ATTCAACTCATT-GAGCTC
1 ATTCAACTCATTCGAGCTC
2003 GTTACTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (20 bp):
ATTCAACTCATTCGAGCTCA
Found at i:2196 original size:32 final size:32
Alignment explanation
Indices: 2159--2238 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
2149 TGTCTTAAGT
* *
2159 CTATTTAATGTGTTTTGTCGTAGTTAATGCTG
1 CTATTTAATGTGTTTTGACGAAGTTAATGCTG
* * * * *
2191 TTATTTAATGCGTCTGGACGAATTTAATGCTG
1 CTATTTAATGTGTTTTGACGAAGTTAATGCTG
*
2223 CTACTTAATGTGTTTT
1 CTATTTAATGTGTTTT
2239 TGCTGCTGTT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.47
Consensus pattern (32 bp):
CTATTTAATGTGTTTTGACGAAGTTAATGCTG
Found at i:7462 original size:24 final size:26
Alignment explanation
Indices: 7413--7475 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
7403 AAGAAGGGCT
*
7413 GAAATTGGCTAAGTGAAATGATGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
*
7439 GAAA-TGGCTAGGTG-AATGAGGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
* *
7463 GAGATTCGCTAAG
1 GAAATTGGCTAAG
7476 GTTTTGAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.39
25 15 0.48
26 4 0.13
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (26 bp):
GAAATTGGCTAAGTGAAATGAGGATG
Found at i:10661 original size:18 final size:18
Alignment explanation
Indices: 10640--10674 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10630 TTTTTCTTTT
10640 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
10658 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
10675 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:11598 original size:32 final size:29
Alignment explanation
Indices: 11552--11622 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 29
11542 GACTTTTCAC
**
11552 TTTTTTTTAACTTGATTTTTTTTTGCTCACCT
1 TTTTTTTTTGCTTGATTTTTTTTT--T-ACCT
*
11584 TTTTTTTTTGCTTGATTTTTTTTTTTCCT
1 TTTTTTTTTGCTTGATTTTTTTTTTACCT
11613 TTTTTTTTTG
1 TTTTTTTTTG
11623 AATTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.36
30 1 0.03
32 22 0.61
ACGTcount: A:0.07, C:0.11, G:0.07, T:0.75
Consensus pattern (29 bp):
TTTTTTTTTGCTTGATTTTTTTTTTACCT
Found at i:11603 original size:17 final size:15
Alignment explanation
Indices: 11583--11621 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
11573 TTTGCTCACC
*
11583 TTTTTTTTTTGCTTGAT
1 TTTTTTTTTTCCTT--T
11600 TTTTTTTTTTCCTTT
1 TTTTTTTTTTCCTTT
11615 TTTTTTT
1 TTTTTTT
11622 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
17 13 0.62
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTCCTTT
Found at i:11615 original size:12 final size:12
Alignment explanation
Indices: 11600--11673 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 12
11590 TTTGCTTGAT
*
11600 TTTTTTTTTTCC
1 TTTTTTTTTTCA
*
11612 TTTTTTTTTTGAA
1 TTTTTTTTTT-CA
11625 TTTTTTTTTTCAATCAA
1 -TTTTTTTTT---TC-A
11642 TTTTTTTTTTCGA
1 TTTTTTTTTTC-A
*
11655 ATTTTTTTTT-A
1 TTTTTTTTTTCA
11666 TTTTTTTT
1 TTTTTTTT
11674 GTTACTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
11 8 0.16
12 10 0.20
13 12 0.24
14 9 0.18
16 9 0.18
17 2 0.04
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:11623 original size:25 final size:26
Alignment explanation
Indices: 11585--11635 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
11575 TGCTCACCTT
*
11585 TTTTTTTTGCTTGATTTTTTTTTTTCC
1 TTTTTTTT-CTTGAATTTTTTTTTTCC
11612 TTTTTTTT-TTGAATTTTTTTTTTC
1 TTTTTTTTCTTGAATTTTTTTTTTC
11636 AATCAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.65
27 8 0.35
ACGTcount: A:0.06, C:0.08, G:0.06, T:0.80
Consensus pattern (26 bp):
TTTTTTTTCTTGAATTTTTTTTTTCC
Found at i:11628 original size:13 final size:13
Alignment explanation
Indices: 11585--11664 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 13
11575 TGCTCACCTT
11585 TTTTTTTTGCTTG-A
1 TTTTTTTT--TTGAA
***
11599 TTTTTTTTTTTCC
1 TTTTTTTTTTGAA
11612 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
*
11625 TTTTTTTTTTCAATCAA
1 -TTTTTTTTT---TGAA
11642 TTTTTTTTTTCGAA
1 TTTTTTTTTT-GAA
11656 TTTTTTTTT
1 TTTTTTTTT
11665 ATTTTTTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
12 2 0.04
13 11 0.21
14 28 0.53
16 9 0.17
17 3 0.06
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:15716 original size:23 final size:22
Alignment explanation
Indices: 15664--15716 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
15654 TCCACGTCTT
*
15664 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
15686 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
15709 TTTCTTTT
1 TTTCTTTT
15717 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:18594 original size:22 final size:22
Alignment explanation
Indices: 18569--18620 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
18559 TTCTTGGCAA
18569 CTTCCTAGAACGTCCCTTGAAG
1 CTTCCTAGAACGTCCCTTGAAG
* * *
18591 CTTCCTTGAAGGTTCCTTGAAG
1 CTTCCTAGAACGTCCCTTGAAG
*
18613 TTTCCTAG
1 CTTCCTAG
18621 CATGGGAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (22 bp):
CTTCCTAGAACGTCCCTTGAAG
Found at i:18599 original size:11 final size:11
Alignment explanation
Indices: 18583--18618 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
18573 CTAGAACGTC
18583 CCTTGAAGCTT
1 CCTTGAAGCTT
*
18594 CCTTGAAGGTT
1 CCTTGAAGCTT
*
18605 CCTTGAAGTTT
1 CCTTGAAGCTT
18616 CCT
1 CCT
18619 AGCATGGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (11 bp):
CCTTGAAGCTT
Found at i:19288 original size:20 final size:20
Alignment explanation
Indices: 19265--19303 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19255 TTCAGGTCAC
*
19265 TCGAGCTCAAGTCAGCTCAT
1 TCGAGCTCAAGTCAACTCAT
19285 TCGAGCTCAAGTCAACTCA
1 TCGAGCTCAAGTCAACTCA
19304 ATCTTAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGAGCTCAAGTCAACTCAT
Found at i:24133 original size:21 final size:21
Alignment explanation
Indices: 24095--24134 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24085 CCACGTCTTT
*
24095 TTCATTTGTTTCTTTTTCTAA
1 TTCATTTGTCTCTTTTTCTAA
24116 TTCATTT-TCTCTTCTTTCT
1 TTCATTTGTCTCTT-TTTCT
24135 TCAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (21 bp):
TTCATTTGTCTCTTTTTCTAA
Done.