Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_806
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: 46032
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:3811 original size:46 final size:46
Alignment explanation
Indices: 3691--3812 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
3681 AACCCGCCCC
* * *
3691 TAAGTGAACTC-GACTCAACTCAACGAGCTCAGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
*
3736 TAAGTGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
*
3782 TAAGTGAACTCGGACTCAACTCAATGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
3813 GGATGCTCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
45 11 0.15
46 60 0.85
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
Found at i:6394 original size:47 final size:46
Alignment explanation
Indices: 6280--6450 Score: 176
Period size: 44 Copynumber: 3.8 Consensus size: 46
6270 GGATGGTTGA
*
6280 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGTAAT
* *
6327 G--TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA-GATGTAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGTAA-T
* * **
6370 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAT
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGTAAT
*
6419 G---CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
6451 TAGGGGGGTT
Statistics
Matches: 106, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 7 0.07
43 1 0.01
44 31 0.29
45 29 0.27
47 30 0.28
48 2 0.02
49 1 0.01
50 5 0.05
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGTAAT
Found at i:6709 original size:19 final size:20
Alignment explanation
Indices: 6672--6709 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6662 ATAAGGTGGT
6672 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
6692 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
6710 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:12503 original size:46 final size:42
Alignment explanation
Indices: 12405--12558 Score: 161
Period size: 46 Copynumber: 3.5 Consensus size: 42
12395 TGGTTGAGCA
* * *
12405 TCCGAACTCG-TGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT-G
1 TCCGAACTCGTTGAG-TGAGTCCGAGTT--C--ATGAATGTAACTAG
*
12450 TCCGAACTCGTTGAGTGAGTCCGAGTTCGTGAGATGTAACTAGG
1 TCCGAACTCGTTGAGTGAGTCCGAGTTCATGA-ATGTAACTA-G
12494 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAATGTAACTAG
1 --TCCGAACTCGTTGAG-TGAGTCCGAGTTCATGAATGTAACTAG
12539 -CCGAACTCGTTGAGTGAGTC
1 TCCGAACTCGTTGAGTGAGTC
12559 GAGCTCACTA
Statistics
Matches: 97, Mismatches: 5, Indels: 18
0.81 0.04 0.15
Matches are distributed among these distances:
41 8 0.08
42 20 0.21
43 1 0.01
44 1 0.01
45 23 0.24
46 28 0.29
47 16 0.16
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
TCCGAACTCGTTGAGTGAGTCCGAGTTCATGAATGTAACTAG
Found at i:14051 original size:42 final size:43
Alignment explanation
Indices: 13990--14200 Score: 276
Period size: 42 Copynumber: 5.0 Consensus size: 43
13980 TATCGTATAG
* *
13990 TACTATTCGGGCTTTGAGCCTAGCAGACTATAATGCCGGTGATA
1 TACTATTCGGCCTTTGAGCCTAGCAG-CTATAATGCCGGTGAGA
14034 -ACTA-TCGGCCTTTGAGCCTAGCAGC--TAATGCCGGTGAGA
1 TACTATTCGGCCTTTGAGCCTAGCAGCTATAATGCCGGTGAGA
*
14073 TACTATTCGGGCCTTTGAGCCTAGCATGCTATAATACCGGTGAGA
1 TACTATTC-GGCCTTTGAGCCTAGCA-GCTATAATGCCGGTGAGA
14118 TAC-ATTCGGCC-TTGAG-CTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGCCTTTGAGCCTAGCA-GCTATAATGCCGGTGAGA
*
14159 TACTATTCTGGCCTTCGAGCCTAGCAGGCTAT-ATGCCGGTGA
1 TACTATTC-GGCCTTTGAGCCTAGCA-GCTATAATGCCGGTGA
14201 AATGATATCG
Statistics
Matches: 151, Mismatches: 6, Indels: 20
0.85 0.03 0.11
Matches are distributed among these distances:
39 13 0.09
40 4 0.03
41 29 0.19
42 45 0.30
43 14 0.09
44 18 0.12
45 28 0.19
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (43 bp):
TACTATTCGGCCTTTGAGCCTAGCAGCTATAATGCCGGTGAGA
Found at i:14098 original size:84 final size:84
Alignment explanation
Indices: 13990--14200 Score: 281
Period size: 86 Copynumber: 2.5 Consensus size: 84
13980 TATCGTATAG
*
13990 TACTATTCGGG-CTTTGAGCCTAGCAGACTATAATGCCGGTGATA-AC-TATCGGCCTTTGAGCC
1 TACTATTCGGGCCTTTGAGCCTAGCAG-CTATAATGCCGGTGAGATACAT-TCGGCC-TTGAG-C
14052 TAGCA-GC-TAATGCCGGTGAGA
62 TAGCAGGCATAATGCCGGTGAGA
*
14073 TACTATTCGGGCCTTTGAGCCTAGCATGCTATAATACCGGTGAGATACATTCGGCCTTGAGCTAG
1 TACTATTCGGGCCTTTGAGCCTAGCA-GCTATAATGCCGGTGAGATACATTCGGCCTTGAGCTAG
14138 CAGGCTATAATGCCGGTGAGA
65 CAGGC-ATAATGCCGGTGAGA
* *
14159 TACTATTCTGGCCTTCGAGCCTAGCAGGCTAT-ATGCCGGTGA
1 TACTATTCGGGCCTTTGAGCCTAGCA-GCTATAATGCCGGTGA
14201 AATGATATCG
Statistics
Matches: 115, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
83 17 0.15
84 36 0.31
85 18 0.16
86 44 0.38
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (84 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGCTATAATGCCGGTGAGATACATTCGGCCTTGAGCTAGC
AGGCATAATGCCGGTGAGA
Found at i:21017 original size:46 final size:46
Alignment explanation
Indices: 20964--21139 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
20954 TGGTTGAGCA
20964 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
21010 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
21055 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
21103 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21140 CGGGTTACAT
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 63 0.56
47 29 0.26
48 3 0.03
50 5 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:21120 original size:93 final size:93
Alignment explanation
Indices: 20961--21132 Score: 326
Period size: 93 Copynumber: 1.8 Consensus size: 93
20951 GAATGGTTGA
*
20961 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
21026 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
21054 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
21119 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
21133 CTTATGGCGG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:25717 original size:24 final size:24
Alignment explanation
Indices: 25690--25739 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
25680 CCATAGCTTT
* *
25690 CCGATATGGTTCTTTGTGCACTTC
1 CCGATAAGGTTCTTTGTGAACTTC
*
25714 CCGATAAGGTTTTTTGTGAACTTC
1 CCGATAAGGTTCTTTGTGAACTTC
25738 CC
1 CC
25740 AATTACGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (24 bp):
CCGATAAGGTTCTTTGTGAACTTC
Found at i:34790 original size:46 final size:46
Alignment explanation
Indices: 34740--34912 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
34730 TGGTTGAGCA
34740 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
34786 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
34831 CATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
34879 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
34913 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.57
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:34896 original size:93 final size:93
Alignment explanation
Indices: 34737--34907 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
34727 GGATGGTTGA
* *
34737 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
34802 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
34830 GCATCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
34895 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
34908 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:37461 original size:21 final size:20
Alignment explanation
Indices: 37429--37471 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
37419 AGATGACATG
*
37429 AAATGTTTGTAATTGTTTTGT
1 AAATGTTTGTAA-TGCTTTGT
37450 AAAT-TTTGGTAATGCTTTGT
1 AAATGTTT-GTAATGCTTTGT
37470 AA
1 AA
37472 CCCTGTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (20 bp):
AAATGTTTGTAATGCTTTGT
Done.