Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_33 ID=scaffold_33-JGI_221_v2.0
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: 46396
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.29
Warning! 3685 characters in sequence are not A, C, G, or T
Found at i:3236 original size:16 final size:16
Alignment explanation
Indices: 3198--3236 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3188 TATTTGACAG
* *
3198 AAAAGTAAAAGAAATA
1 AAAAGCAAAAGAAAGA
3214 AAAAGCAAAAGAAAGA
1 AAAAGCAAAAGAAAGA
*
3230 AACAGCA
1 AAAAGCA
3237 GTCGAGCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.08, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAGCAAAAGAAAGA
Found at i:9740 original size:132 final size:132
Alignment explanation
Indices: 9498--9783 Score: 432
Period size: 132 Copynumber: 2.2 Consensus size: 132
9488 CTATAAATCT
* * *
9498 TATCTCCCTGAACAGCAGTTGAATAGGTGGAAGATTGTAAGTCCTAGCTCCCTGAACAGCAGTAG
1 TATCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCAAGTCCTAGCTCCCTGAACAGCAATAG
*
9563 AATAGGTGGAAGATTGCATGTCCTAGCTACCTGAACAACATTGGAATAGGTGGAAAATTGTATG-
66 AATAGGTGGAAGATTGCATGTCCTAGCTACCTGAACAACAGTGGAATAGGTGGAAAATTGTA-GA
9627 TCC
130 TCC
* *
9630 TATCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAGCTCCCTGAACAGCAATGG
1 TATCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCAAGTCCTAGCTCCCTGAACAGCAATAG
* * * *
9695 AATAGGTGGAAGATTGCATGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGTAAGATTGTAGAT
66 AATAGGTGGAAGATTGCATGTCCTAGCTACCTGAACAACAGTGGAATAGGTGGAAAATTGTAGAT
9760 CC
131 CC
* *
9762 TGTCTCCCT-AAGCAGTAGTGGA
1 TATCTCCCTGAA-CAGCAGTGGA
9784 GCAGATCGAA
Statistics
Matches: 140, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
131 3 0.02
132 137 0.98
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (132 bp):
TATCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCAAGTCCTAGCTCCCTGAACAGCAATAG
AATAGGTGGAAGATTGCATGTCCTAGCTACCTGAACAACAGTGGAATAGGTGGAAAATTGTAGAT
CC
Found at i:9783 original size:44 final size:44
Alignment explanation
Indices: 9501--9754 Score: 400
Period size: 44 Copynumber: 5.8 Consensus size: 44
9491 TAAATCTTAT
* * *
9501 CTCCCTGAACAGCAGTTGAATAGGTGGAAGATTGTAAGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
*
9545 CTCCCTGAACAGCAGTAGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
* * * * * *
9589 CTACCTGAACAACATTGGAATAGGTGGAAAATTGTATGTCCTAT
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
9633 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
*
9677 CTCCCTGAACAGCAATGGAATAGGTGGAAGATTGCATGTCCTAG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
*
9721 CTCCCTGAACAGCAGTGGAATAGGTGTAAGATTG
1 CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
9755 TAGATCCTGT
Statistics
Matches: 191, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 191 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (44 bp):
CTCCCTGAACAGCAGTGGAATAGGTGGAAGATTGCATGTCCTAG
Found at i:11527 original size:23 final size:23
Alignment explanation
Indices: 11487--11532 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11477 ACCCACCTAT
11487 TTTTATTTATATACATTATTTTA
1 TTTTATTTATATACATTATTTTA
*
11510 TTTTA-TTATGTACTATTATTTTA
1 TTTTATTTATATAC-ATTATTTTA
11533 ATTCTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTATTTATATACATTATTTTA
Found at i:15353 original size:43 final size:43
Alignment explanation
Indices: 15238--15353 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
15228 GAATCATACA
* *
15238 CGATGCCAAT-TCCCAAACATGGTCTTGCACGTTTCCCCACTT
1 CGATGCCAATGTCCCAAACATGGTCTTACAGGTTTCCCCACTT
* *
15280 CGATGCCAATGTCTCAAACATGGTCTTACAGGTTTCCTCACTT
1 CGATGCCAATGTCCCAAACATGGTCTTACAGGTTTCCCCACTT
* *
15323 CGATGCCAATGTCCCAGACATTGTCTTACAG
1 CGATGCCAATGTCCCAAACATGGTCTTACAG
15354 CTCAGAAGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
42 10 0.15
43 56 0.85
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.29
Consensus pattern (43 bp):
CGATGCCAATGTCCCAAACATGGTCTTACAGGTTTCCCCACTT
Found at i:15559 original size:32 final size:32
Alignment explanation
Indices: 15518--15857 Score: 464
Period size: 32 Copynumber: 10.6 Consensus size: 32
15508 TCGGTAATAG
15518 CAATTCAATTCGGCAATATAAGTATACATATA
1 CAATTCAATTCGGCAATATAAGTATACATATA
*** *
15550 CAATTCAATTCGGCAATAGGTGTATACCTATA
1 CAATTCAATTCGGCAATATAAGTATACATATA
*
15582 CAATTCAATTCGGCAATATAAGTATACATACA
1 CAATTCAATTCGGCAATATAAGTATACATATA
*** * *
15614 CAATTCAATTCGGCAATAGGTGTATACCTAAA
1 CAATTCAATTCGGCAATATAAGTATACATATA
*
15646 CAATTCAATTCAGCAATATAAGTATACATATA
1 CAATTCAATTCGGCAATATAAGTATACATATA
*** *
15678 CAATTCAATTCGGCAATAGGTGTATACCTATA
1 CAATTCAATTCGGCAATATAAGTATACATATA
* *
15710 CAATTCAATTTGGCAATATAAGTATACATACA
1 CAATTCAATTCGGCAATATAAGTATACATATA
* *
15742 CAATTCAATTCGCCAATATAAGTATACATATG
1 CAATTCAATTCGGCAATATAAGTATACATATA
*** *
15774 CAATTCAATTCGGCAATAGGTGTATACCTATA
1 CAATTCAATTCGGCAATATAAGTATACATATA
*
15806 CAATTTAATTCGGCAATATAAGTATACATATA
1 CAATTCAATTCGGCAATATAAGTATACATATA
15838 CAATTCAATTCGGCAATATA
1 CAATTCAATTCGGCAATATA
15858 TAAAACATAT
Statistics
Matches: 261, Mismatches: 47, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 261 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (32 bp):
CAATTCAATTCGGCAATATAAGTATACATATA
Found at i:18825 original size:84 final size:84
Alignment explanation
Indices: 18667--18835 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 84
18657 GTCCAGCTTA
* * * * *
18667 TTACATCCATTTAATGAGTCCTAGTTCCAGCAAAAATTAATAGGAAGGTTAATGTGTCTTAGCGG
1 TTACATCCATTTAATGAGTCATAGTTCCAGCAAAAATTAAGAGCAAGGTTAAAGTGTCTTAACGG
*
18732 CTGCCGAATTCATTAAATC
66 CTGCAGAATTCATTAAATC
* * ** *
18751 TTACATCTATTTAATGTGTCATAGTTCCAGCCGAAATTAAGAGCAAGGTTAAAGTGTCTTAATGG
1 TTACATCCATTTAATGAGTCATAGTTCCAGCAAAAATTAAGAGCAAGGTTAAAGTGTCTTAACGG
* * *
18816 TTGCAGAATTTATTATATC
66 CTGCAGAATTCATTAAATC
18835 T
1 T
18836 CAAGCTGATG
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (84 bp):
TTACATCCATTTAATGAGTCATAGTTCCAGCAAAAATTAAGAGCAAGGTTAAAGTGTCTTAACGG
CTGCAGAATTCATTAAATC
Found at i:21790 original size:14 final size:14
Alignment explanation
Indices: 21763--21805 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
21753 GATAGGTCGC
21763 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
21775 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
21789 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
21803 ATG
1 ATG
21806 CGTACAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.24
13 1 0.03
14 21 0.72
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:21795 original size:115 final size:115
Alignment explanation
Indices: 21675--21903 Score: 277
Period size: 115 Copynumber: 2.0 Consensus size: 115
21665 GCACAGATTG
* *
21675 TGTGTAGGCCATTAT-GTAAAAGTGAAAGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCCAC
1 TGTGTAGGCCACTATCGT-AAAG-GAAAGT-ATCGATCACGTGTGTAGTACTATGTGCAGGCCAC
* *
21738 TACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGTACTATGTGTAGGCTACTA
63 TACGTGTACCGG-ATGATAATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
* * * * *
21790 TGTGTAGGCTACTATGCGTACAGGATAGTTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGGCCACTAT-CGTAAAGGAAAGTATCGATCACGTGTGTAGTACTATGTGCAGGCCACTA
* * *
21855 TGTGTATCGGATGATAATGGTCACATGTGTAGTACTATTTGCAGGCTAC
65 CGTGTACCGGATGATAATGGTCACATGTGTAGTACTATGTGCAGGCTAC
21904 CATGCAAACC
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
114 6 0.06
115 58 0.60
116 31 0.32
117 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (115 bp):
TGTGTAGGCCACTATCGTAAAGGAAAGTATCGATCACGTGTGTAGTACTATGTGCAGGCCACTAC
GTGTACCGGATGATAATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
Found at i:21980 original size:45 final size:45
Alignment explanation
Indices: 21911--22005 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
21901 TACCATGCAA
*
21911 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
21956 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
22001 ACCGA
1 ACCGA
22006 GTATCTGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:28854 original size:19 final size:17
Alignment explanation
Indices: 28827--28866 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
28817 TTTCTTAAAT
28827 AATTATAATAATCATTTAA
1 AATTATAATAA--ATTTAA
*
28846 AATTGTAATAAATTTAA
1 AATTATAATAAATTTAA
28863 AATT
1 AATT
28867 TTATTACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
AATTATAATAAATTTAA
Found at i:29079 original size:28 final size:27
Alignment explanation
Indices: 29047--29100 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
29037 ACCATTATTA
29047 ATAATTTTAAAATAAATTTCTATATTTT
1 ATAATTTTAAAAT-AATTTCTATATTTT
* *
29075 ATAATTTTATAATAATTTTTATATTT
1 ATAATTTTAAAATAATTTCTATATTT
29101 ATTTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
ATAATTTTAAAATAATTTCTATATTTT
Found at i:30394 original size:22 final size:22
Alignment explanation
Indices: 30352--30394 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30342 TCTCCCTATT
*
30352 TTGCTACCATTTTACTGTTATG
1 TTGCTACCATTTTACTATTATG
* *
30374 TTGCTACTATTTTATTATTAT
1 TTGCTACCATTTTACTATTAT
30395 TGTTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTTACTATTATG
Found at i:30458 original size:30 final size:30
Alignment explanation
Indices: 30424--30486 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
30414 ACTTATTTTA
30424 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
30454 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
30484 TTG
1 TTG
30487 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:30640 original size:12 final size:12
Alignment explanation
Indices: 30610--30642 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
30600 TATATATTTG
30610 AAAATT-ATATA
1 AAAATTAATATA
30621 AAAA-TAATATA
1 AAAATTAATATA
30632 AAAATTAATAT
1 AAAATTAATAT
30643 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:38246 original size:25 final size:25
Alignment explanation
Indices: 38218--38274 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
38208 TAGTTTCTCG
* *
38218 AAAATTTAATAGGGGCAAAATTGTC
1 AAAATTTAACAGGGGCAAAATAGTC
* *
38243 AAAATTTACCAGGGGTAAAATAGTC
1 AAAATTTAACAGGGGCAAAATAGTC
38268 AAAATTT
1 AAAATTT
38275 TGTTGGGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.28
Consensus pattern (25 bp):
AAAATTTAACAGGGGCAAAATAGTC
Done.