Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1897
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: 27654
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2037 original size:68 final size:68
Alignment explanation
Indices: 1887--2043 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 68
1877 CTAGCCAATT
* * *
1887 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
1952 TTTA
65 CATA
* * *
1956 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
2018 CTACATA
63 C-ACATA
2025 GTATCTCGTAGCT-TCTTGT
1 -TATCTCGTAGCTCTCTTGT
2044 ACACATGATG
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
67 6 0.08
68 29 0.39
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:9506 original size:68 final size:67
Alignment explanation
Indices: 9356--9513 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 67
9346 CTAGCCAATT
* *
9356 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTT-G-ATCACACATGCGACCTAGCTACA
**
9421 TTTA
64 CATA
* *
9425 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-CTAT-ATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACT-TGATCACACATGCGACCTAGCTA
9487 CTACATA
62 C-ACATA
*
9494 GTATCTCGTAGCTTTCTTGT
1 -TATCTCGTAGCTCTCTTGT
9514 ACACATGATA
Statistics
Matches: 75, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
68 34 0.45
69 7 0.09
70 7 0.09
71 27 0.36
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (67 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTTGATCACACATGCGACCTAGCTACACA
TA
Found at i:17671 original size:26 final size:26
Alignment explanation
Indices: 17636--17686 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
17626 AATGTGAAAG
*
17636 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
17662 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
17687 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:17724 original size:103 final size:102
Alignment explanation
Indices: 17559--17778 Score: 363
Period size: 103 Copynumber: 2.2 Consensus size: 102
17549 TGTATATAAA
** * *
17559 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
17624 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
17661 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
17725 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
17764 AGGGGTT-CTAAGTGC
1 AGGGGTTGCTAAGTGC
17779 GATATCCATT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
102 35 0.32
103 75 0.68
104 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:17843 original size:26 final size:26
Alignment explanation
Indices: 17808--17859 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
17798 AAATGAAAAG
* *
17808 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
17834 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
17860 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:17845 original size:70 final size:71
Alignment explanation
Indices: 17699--17847 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 71
17689 TCATTGGTGG
* *
17699 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
17764 AGGGGT
66 AGGGGT
***
17770 T-CTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
17833 AGGGGT
66 AGGGGT
17839 TGCTAAGTG
1 TGCTAAGTG
17848 ATGATTCCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 36 0.50
70 35 0.49
71 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
AGGGGT
Found at i:25266 original size:103 final size:103
Alignment explanation
Indices: 25097--25317 Score: 317
Period size: 103 Copynumber: 2.2 Consensus size: 103
25087 TGTATATAAA
** * *
25097 AGGGGTTGCTGTGTGCTGATTCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTTT
1 AGGGGTTGCTAAGTGCTGATTCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTT
25162 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
25200 AGGGGTTGCTAAGTGCTGATTCCCTCGGTTCATTGTGGTGCTAAGTGCGAT-AT-CACCA-ATAC
1 AGGGGTTGCTAAGTGCTGATT-CC-CGATTCATGGTGGTGCTAAGTGCG-TGATCCACCATAT-C
25262 -TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
62 TTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
25303 AGGGGTT-CTAAGTGC
1 AGGGGTTGCTAAGTGC
25318 GATATCCATT
Statistics
Matches: 108, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
102 8 0.07
103 69 0.64
104 8 0.07
105 22 0.20
106 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.32
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:25294 original size:76 final size:70
Alignment explanation
Indices: 25236--25385 Score: 200
Period size: 70 Copynumber: 2.2 Consensus size: 70
25226 GGTTCATTGT
*
25236 GGTGCTAAGTGCGATAT-CA-CCAATACTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCC
1 GGTGCTAAGTGCGATATCCATCCAATA-TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCC
25299 CCCGAGG
64 CCCGAGG
* ***
25306 GGTTCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATT-CCC
1 GGTGCTAAGTGCGATATCCATCCAATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCC
25370 C-AGG
66 CGAGG
25374 GGTTGCTAAGTG
1 GG-TGCTAAGTG
25386 ATGATTCCCC
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
68 5 0.07
69 12 0.17
70 40 0.56
71 11 0.15
72 3 0.04
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (70 bp):
GGTGCTAAGTGCGATATCCATCCAATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCC
CGAGG
Found at i:25380 original size:25 final size:25
Alignment explanation
Indices: 25347--25395 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
25337 AAATGAAAAG
* *
25347 GGGGTTGCTATGTGCTGATTCCCCA
1 GGGGTTGCTAAGTGATGATTCCCCA
25372 GGGGTTGCTAAGTGATGATTCCCC
1 GGGGTTGCTAAGTGATGATTCCCC
25396 GATTCAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (25 bp):
GGGGTTGCTAAGTGATGATTCCCCA
Done.