Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold591
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: 49382
ACGTcount: A:0.18, C:0.09, G:0.10, T:0.19
Warning! 21271 characters in sequence are not A, C, G, or T
Found at i:65 original size:3 final size:3
Alignment explanation
Indices: 57--97 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
47 ATCTAGTTTT
57 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
98 CAATTAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:255 original size:42 final size:42
Alignment explanation
Indices: 196--279 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
186 TCAATTTGAT
196 TTGGATAAAACAAATCCCATGTGAAAAAATCGAACTCAAGCC
1 TTGGATAAAACAAATCCCATGTGAAAAAATCGAACTCAAGCC
*
238 TTGGATAAAACAAATCCCATGTGAAAAAATCGAACTCGAGCC
1 TTGGATAAAACAAATCCCATGTGAAAAAATCGAACTCAAGCC
280 GAATTGTGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19
Consensus pattern (42 bp):
TTGGATAAAACAAATCCCATGTGAAAAAATCGAACTCAAGCC
Found at i:1766 original size:28 final size:30
Alignment explanation
Indices: 1724--1780 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
1714 ACCATAGTGC
1724 CACTGTCAGTTGCATCAAAGTGCCACTTTT
1 CACTGTCAGTTGCATCAAAGTGCCACTTTT
* *
1754 CACTG-CA-TTGCATTAAAGTTCCACTTT
1 CACTGTCAGTTGCATCAAAGTGCCACTTT
1781 CCATTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.72
29 2 0.08
30 5 0.20
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (30 bp):
CACTGTCAGTTGCATCAAAGTGCCACTTTT
Found at i:24710 original size:102 final size:102
Alignment explanation
Indices: 24568--24754 Score: 277
Period size: 102 Copynumber: 1.8 Consensus size: 102
24558 AATGCTATTC
* *
24568 GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCA-ATACCATCCGGTACACGTAGTA
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCATA-ACCATCCGATACACATAGTA
*
24632 GCCTGCACATAGTACTACACACTTGACCAAAGCTATCT
65 GCCTACACATAGTACTACACACTTGACCAAAGCTATCT
* * * ** *
24670 GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAACTATCTTATACTCATAGTAG
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCATAACCATCCGATACACATAGTAG
24735 CCTACACATAGTACTACACA
66 CCTACACATAGTACTACACA
24755 TGAGTTCTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
102 74 0.99
103 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (102 bp):
GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCATAACCATCCGATACACATAGTAG
CCTACACATAGTACTACACACTTGACCAAAGCTATCT
Found at i:24755 original size:51 final size:50
Alignment explanation
Indices: 24568--24756 Score: 236
Period size: 51 Copynumber: 3.7 Consensus size: 50
24558 AATGCTATTC
* * * *
24568 GGTACACATAGTAGCCTACACTTAGTACTACACACGTGACCAATACCATCC
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAA-ACTATCT
* *
24619 GGTACACGTAGTAGCCTGCACATAGTACTACACACT-TGACCAAAGCTATCT
1 GGTACACATAGTAGCCTACACATAGTACTACACA-TGTGACCAAA-CTATCT
* *
24670 GGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAACTATCT
1 GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCA-AACTATCT
** *
24721 TATACTCATAGTAGCCTACACATAGTACTACACATG
1 GGTACACATAGTAGCCTACACATAGTACTACACATG
24757 AGTTCTCATG
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
50 2 0.02
51 117 0.97
52 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (50 bp):
GGTACACATAGTAGCCTACACATAGTACTACACATGTGACCAAACTATCT
Found at i:27726 original size:84 final size:85
Alignment explanation
Indices: 27619--27789 Score: 326
Period size: 84 Copynumber: 2.0 Consensus size: 85
27609 TCTTGATGAA
27619 CCTTCATACAAAACCCGAGCCAAAAACGTTAATTTGTATTTACCCTTTTCTTTTGGTCCTAAACT
1 CCTTCATAC-AAACCCGAGCCAAAAACGTTAATTTGTATTTACCCTTTTCTTTTGGTCCTAAACT
27684 GCACGACTATAGACATCTGAC
65 GCACGACTATAGACATCTGAC
27705 CCTTCATAC-AACCCGAGCCAAAAACGTTAATTTGTATTTACCCTTTTCTTTTGGTCCTAAACTG
1 CCTTCATACAAACCCGAGCCAAAAACGTTAATTTGTATTTACCCTTTTCTTTTGGTCCTAAACTG
27769 CACGACTATAGACATCTGAC
66 CACGACTATAGACATCTGAC
27789 C
1 C
27790 ATACATATTG
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 76 0.89
86 9 0.11
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (85 bp):
CCTTCATACAAACCCGAGCCAAAAACGTTAATTTGTATTTACCCTTTTCTTTTGGTCCTAAACTG
CACGACTATAGACATCTGAC
Found at i:41011 original size:18 final size:18
Alignment explanation
Indices: 40977--41025 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
40967 CGCAATAAAA
40977 AACGTTTGGAAATTGAAT
1 AACGTTTGGAAATTGAAT
*
40995 AACGATTTGTAAA-TGAAT
1 AACG-TTTGGAAATTGAAT
*
41013 AATGTTTTGGAAA
1 AACG-TTTGGAAA
41026 CGAACGACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (18 bp):
AACGTTTGGAAATTGAAT
Found at i:44979 original size:19 final size:19
Alignment explanation
Indices: 44955--44994 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
44945 ACAGGCAACA
*
44955 AAGAATTCCCAATTCATGT
1 AAGAATTCCCAATTCACGT
44974 AAGAATTCCCAATTCACGT
1 AAGAATTCCCAATTCACGT
44993 AA
1 AA
44995 AATCAATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (19 bp):
AAGAATTCCCAATTCACGT
Found at i:46298 original size:22 final size:22
Alignment explanation
Indices: 46273--46315 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
46263 AACTTAATTC
*
46273 ACATTTATTGATTGAATGTAAT
1 ACATTTATTAATTGAATGTAAT
46295 ACATTTATTAATTGAATGTAA
1 ACATTTATTAATTGAATGTAA
46316 AGAAGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ACATTTATTAATTGAATGTAAT
Done.