Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1740
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: 41695
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10904 original size:18 final size:19
Alignment explanation
Indices: 10883--10929 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
10873 ATATATGGAT
10883 ATATATAATAGGAT-ATAA
1 ATATATAATAGGATGATAA
* *
10901 ATATATAATAAGATGATAT
1 ATATATAATAGGATGATAA
10920 ATATA-AATAG
1 ATATATAATAG
10930 TTATAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (19 bp):
ATATATAATAGGATGATAA
Found at i:10935 original size:35 final size:33
Alignment explanation
Indices: 10880--10944 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
10870 GAGATATATG
10880 GATATATATAATAGGATATAAATATATAATAAGAT
1 GATATATATAATAGGATAT-AATA-ATAATAAGAT
*
10915 GATATATATAAATA-GTTATAATAATAATAA
1 GATATATAT-AATAGGATATAATAATAATAA
10945 TAATAATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 4 0.14
35 13 0.46
36 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.35
Consensus pattern (33 bp):
GATATATATAATAGGATATAATAATAATAAGAT
Found at i:12160 original size:15 final size:15
Alignment explanation
Indices: 12140--12176 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
12130 GGGCATGGTA
12140 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
12155 ATTGGGTTTGTGGGT
1 ATTGGGTTTGTGGGT
12170 ATTGGGT
1 ATTGGGT
12177 CCCTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (15 bp):
ATTGGGTTTGTGGGT
Found at i:13695 original size:132 final size:131
Alignment explanation
Indices: 13453--13919 Score: 401
Period size: 132 Copynumber: 3.5 Consensus size: 131
13443 AGAAAATCGA
* * * * * * **
13453 AACCCAGCAC-AGTAGGGCAC-AGTTCTTCGAATTTCTAAACATCGAGCATTGCCTT-ATTTTTT
1 AACCCAGCACGA-TAGGGCACGA-TTCCTCGAATTGCCAAACATCGAACATTACCTTCGTTTTAA
* * * * ** * *
13515 AGAGTTTTGAAGAAACATGAGGGAAATTCTAAAGGGGATGTTCAATTATTTTAAACCAATAG-GA
64 AGAGTTTTTAA-AAACATAAGTGAAATTC-AAAAGGGACCTTCGATTATTTT-AACAAATAGAGA
13579 AATTGC
126 AATTGC
**
13585 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGTTTTGGAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAG
*
13650 AGTTTTTAGAAAACATAAGTGTAATTCAAAAGGGACCTTCGATTATTTTGAACAAAT-GAGAAAT
66 AGTTTTTA-AAAACATAAGTGAAATTCAAAAGGGACCTTCGATTATTTT-AACAAATAGAGAAAT
13714 TGC
129 TGC
* * * * * *
13717 AACCCAGCACGATAGGGCACTATTCCGCGAATTGTCGAATATCGAACATCACCTTCG-TTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAG
* * * * * ** *
13781 -GATTTTTAAAAGACATAGGTGAAATTCTAGAGGGACCCTCGATTACTTTGAGTAAA-CGAGAAA
66 AG-TTTTTAAAA-ACATAAGTGAAATTCAAAAGGGACCTTCGATTA-TTTTAACAAATAGAGAAA
13844 TTGC
128 TTGC
* ** * * * ** *
13848 AACCCAACACTTTAGGGCACGATTCCTCGAATTGCCAAATATCGGATATCGCCTTAGTTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAG
*
13913 AATTTTT
66 AGTTTTT
13920 TTTTAAAAAA
Statistics
Matches: 278, Mismatches: 46, Indels: 22
0.80 0.13 0.06
Matches are distributed among these distances:
130 4 0.01
131 100 0.36
132 144 0.52
133 29 0.10
134 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (131 bp):
AACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGTTTTAAAG
AGTTTTTAAAAACATAAGTGAAATTCAAAAGGGACCTTCGATTATTTTAACAAATAGAGAAATTG
C
Found at i:13867 original size:131 final size:131
Alignment explanation
Indices: 13577--13919 Score: 411
Period size: 131 Copynumber: 2.6 Consensus size: 131
13567 AAACCAATAG
* *
13577 GAAATTGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCG
1 GAAATTGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAATATCGAACATCACCTTCG
** * * *
13642 TTT-TGGAGAGTTTTTAGAAAACATAAGTGTAATTCAAAAGGGACCTTCGATTATTTTGAACAAA
66 TTTAAAG-GA-TTTTTAGAAAACATAAGTGAAATTCAAAAGGGACCCTCGATTACTTTGAACAAA
*
13706 TGA
129 CGA
* * * *
13709 GAAATTGCAACCCAGCACGATAGGGCACTATTCCGCGAATTGTCGAATATCGAACATCACCTTCG
1 GAAATTGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAATATCGAACATCACCTTCG
* * * **
13774 TTTAAAGGATTTTTA-AAAGACATAGGTGAAATTCTAGAGGGACCCTCGATTACTTTGAGTAAAC
66 TTTAAAGGATTTTTAGAAA-ACATAAGTGAAATTCAAAAGGGACCCTCGATTACTTTGAACAAAC
13838 GA
130 GA
* ** * * * *
13840 GAAATTGCAACCCAACACTTTAGGGCACGATTCCTCGAATTGCCAAATATCGGATATCGCCTTAG
1 GAAATTGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAATATCGAACATCACCTTCG
*
13905 TTTTAAAGAATTTTT
66 -TTTAAAGGATTTTT
13920 TTTTAAAAAA
Statistics
Matches: 179, Mismatches: 29, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
130 3 0.02
131 98 0.55
132 77 0.43
133 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (131 bp):
GAAATTGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAATATCGAACATCACCTTCG
TTTAAAGGATTTTTAGAAAACATAAGTGAAATTCAAAAGGGACCCTCGATTACTTTGAACAAACG
A
Found at i:25302 original size:15 final size:14
Alignment explanation
Indices: 25284--25314 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
25274 AATTTGTGTG
25284 TTTTTTATTTTTATT
1 TTTTTTATTTTT-TT
25299 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
25313 TT
1 TT
25315 CAAAAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTATTTTTTT
Found at i:34247 original size:2 final size:2
Alignment explanation
Indices: 34240--34277 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
34230 TCAAAACTTT
34240 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34278 CTCACTTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:34477 original size:27 final size:25
Alignment explanation
Indices: 34447--34516 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 25
34437 TTCATTTAAC
34447 ATATTATTTATTTGAAATTTGCCTTAT
1 ATATTATTTATTTGAAA-TTG-CTTAT
** *
34474 ATATTATTTTATTCCAAATTGTTTAT
1 ATATTA-TTTATTTGAAATTGCTTAT
*
34500 ATTTTATTTATGTTGAA
1 ATATTATTTAT-TTGAA
34517 TTTTTTTCAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.14
26 12 0.34
27 9 0.26
28 9 0.26
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.57
Consensus pattern (25 bp):
ATATTATTTATTTGAAATTGCTTAT
Found at i:36075 original size:52 final size:48
Alignment explanation
Indices: 35998--36202 Score: 184
Period size: 47 Copynumber: 4.2 Consensus size: 48
35988 CATGGCAGCA
* * * * * *
35998 TGTGAAATGTGATTTCGTATAAGACCATAGCTGGGCTACGGCTTCGGAG
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG
* *
36047 AAATGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCG-G
1 ---TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
* * *
36097 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATC-AG
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
* * * * *
36144 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCG-G
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
36190 TATGTGATATGTG
1 --TGTGATATGTG
36203 ACTATGTGCA
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
46 26 0.20
47 54 0.42
48 11 0.08
50 1 0.01
51 1 0.01
52 37 0.28
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (48 bp):
TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
Found at i:36119 original size:47 final size:47
Alignment explanation
Indices: 36050--36202 Score: 191
Period size: 47 Copynumber: 3.2 Consensus size: 47
36040 TTCGGAGAAA
* *
36050 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGG
1 TGTGATATGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGG
* *
36097 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATCAG
1 TGTGATATGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGG
* * ** * *
36144 TGTGATATGTGAT-CCGTGTAAGACCATGGCTGGGCTATGGCCTCGG
1 TGTGATATGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGG
36190 TATGTGATATGTG
1 --TGTGATATGTG
36203 ACTATGTGCA
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
46 26 0.28
47 55 0.60
48 11 0.12
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (47 bp):
TGTGATATGTGCTACCGTATAAGACCATATCTGGGATATGGCATCGG
Done.