Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2066
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: 28274
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Found at i:6034 original size:16 final size:16
Alignment explanation
Indices: 6006--6046 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5996 TTGAAATATC
6006 ATTTTCTTT-TTAAACA
1 ATTTT-TTTATTAAACA
6022 ATTTTTTTATTAAACA
1 ATTTTTTTATTAAACA
*
6038 ACTTTTTTA
1 ATTTTTTTA
6047 AATCTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTTTATTAAACA
Found at i:6769 original size:29 final size:30
Alignment explanation
Indices: 6694--6769 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
6684 AGTTTATATT
*
6694 AAATAAATTTTTAAGTTTTAATTTTTATCTA
1 AAAT-AATTTTTAATTTTTAATTTTTATCTA
** *
6725 AAATTGTTTTAAATTTTTAATTTTTATC-A
1 AAATAATTTTTAATTTTTAATTTTTATCTA
*
6754 AAATAATTTTTTATTT
1 AAATAATTTTTAATTT
6770 ATATTTAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 13 0.35
30 20 0.54
31 4 0.11
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (30 bp):
AAATAATTTTTAATTTTTAATTTTTATCTA
Found at i:6784 original size:23 final size:23
Alignment explanation
Indices: 6734--6785 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
6724 AAAATTGTTT
*
6734 TAAATTTTTAATTTTTATCAAAA
1 TAAATTTTTAATTTATATCAAAA
* **
6757 T-AATTTTTTATTTATATTTAAA
1 TAAATTTTTAATTTATATCAAAA
6779 TAAATTT
1 TAAATTT
6786 GAAGTACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAATTTTTAATTTATATCAAAA
Found at i:7901 original size:12 final size:12
Alignment explanation
Indices: 7884--7908 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7874 AGCCTTATAC
7884 TTTAGTCAAAGA
1 TTTAGTCAAAGA
7896 TTTAGTCAAAGA
1 TTTAGTCAAAGA
7908 T
1 T
7909 GTCTATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:15740 original size:228 final size:230
Alignment explanation
Indices: 15232--15928 Score: 1049
Period size: 228 Copynumber: 3.0 Consensus size: 230
15222 AGGCATTGAC
* * * ** * *
15232 AACCCGTTCTAGCAAGGAAACTGGTGAAAGAGGATTTCTGAATGATTTGTCCATTTTTCCAAGCT
1 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCA--TTTCCAAGCT
* * *
15297 GTTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAAGCAAGGTGATGGATTTGGCCTTGGTGTT
64 ATTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTT
*
15362 CTGGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCT
129 CCGGATTTC-TTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCT
** *
15427 TGTAGTTTGTCCGATAGGCCAAGTGGATGACAATGAAGCA
193 TGTAG--TGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
* * *
15467 AACCAGTTCTAGAAAGGATGCTGGTGAAAGAGTTTTTTGGAATGATTCGTCCACTTCCAAGCTAT
1 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGCTAT
15532 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGA-TTGGCCTTGGTGTTCC
66 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTCC
* * *
15596 CGATTTCGTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTGTAATGTATTCTGCTTGCCTCCTTG
131 GGATTTC-TTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTG
15661 T-G-GTTAGATAGGCCAAGTGGAAGACAATGAAGCA
195 TAGTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
*
15695 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGCAAT
1 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGCTAT
* * *
15760 TCTTTTTATTAAGCCAATTGATTTAGAGTGAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTCC
66 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTCC
*
15825 GGATTTCTGTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGCATTCTGCTTGCCTTCTTG
131 GGATTTCT-TTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTG
* *
15890 TAGTTTGTTAAATAGGCCAAGTGGTAGACAATGAAGCA
195 TAG--TGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
15928 A
1 A
15929 TGGGTTTTGC
Statistics
Matches: 422, Mismatches: 34, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
228 136 0.32
229 76 0.18
230 1 0.00
231 1 0.00
232 77 0.18
233 87 0.21
235 44 0.10
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (230 bp):
AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGCTAT
TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTCC
GGATTTCTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTGT
AGTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
Found at i:23998 original size:29 final size:29
Alignment explanation
Indices: 23953--24038 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
23943 TAAGCGATAA
* *
23953 TTTTAGTTTATAT-TAAATAAATTTTTAAG
1 TTTTAATTT-TATCTAAATAATTTTTTAAG
*
23982 TTTTAATTTTATCT-AA-AATTGTTTTAAAT
1 TTTTAATTTTATCTAAATAATT-TTTT-AAG
*
24011 TTTTAATTTTTATCAAAATAATTTTTTA
1 TTTTAA-TTTTATCTAAATAATTTTTTA
24039 TTTATATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
27 3 0.06
28 9 0.19
29 17 0.36
30 8 0.17
31 6 0.13
32 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
TTTTAATTTTATCTAAATAATTTTTTAAG
Found at i:24041 original size:29 final size:29
Alignment explanation
Indices: 23967--24041 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
23957 AGTTTATATT
*
23967 AAATAAATTTTTAAGTTTTAATTTTATCTA
1 AAAT-AATTTTTAATTTTTAATTTTATCTA
** *
23997 AAATTGTTTTAAATTTTTAATTTTTATC-A
1 AAATAATTTTTAATTTTTAA-TTTTATCTA
*
24026 AAATAATTTTTTATTT
1 AAATAATTTTTAATTT
24042 ATATTTAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (29 bp):
AAATAATTTTTAATTTTTAATTTTATCTA
Found at i:24056 original size:23 final size:23
Alignment explanation
Indices: 24006--24057 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
23996 AAAATTGTTT
*
24006 TAAATTTTTAATTTTTATCAAAA
1 TAAATTTTTAATTTATATCAAAA
* **
24029 T-AATTTTTTATTTATATTTAAA
1 TAAATTTTTAATTTATATCAAAA
24051 TAAATTT
1 TAAATTT
24058 GAAGTACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAATTTTTAATTTATATCAAAA
Found at i:25173 original size:12 final size:12
Alignment explanation
Indices: 25156--25180 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25146 AGCCTTATAC
25156 TTTAGTCAAAGA
1 TTTAGTCAAAGA
25168 TTTAGTCAAAGA
1 TTTAGTCAAAGA
25180 T
1 T
25181 GTCTATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Done.