Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_379 ID=scaffold_379-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: 7882
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.32
Warning! 207 characters in sequence are not A, C, G, or T
Found at i:3857 original size:50 final size:50
Alignment explanation
Indices: 3734--4022 Score: 282
Period size: 51 Copynumber: 5.7 Consensus size: 50
3724 ACCGAGAAGC
* * *
3734 TTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCG-ATAAA
1 TTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAT-AA
* * * * *
3784 TGATGGCCACGTGTGTAGTACTATGTGAAGGCTATTACGTGAATCGTAA-AA
1 T-TTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG-AATAA
* *
3835 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGA
1 TTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATAA
* * * ***
3886 -TGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATACGTA-CTGAATAGA
1 TTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATA-A
* *
3936 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAA
1 TTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAT--AA
* * *
3988 -ATGGTCACATGTGTAGTACTACGTGCAGGCTACTA
1 TTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
4023 TGTGAACCGG
Statistics
Matches: 195, Mismatches: 34, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
49 5 0.03
50 75 0.38
51 111 0.57
52 2 0.01
53 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
TTTGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAA
Found at i:3939 original size:101 final size:101
Alignment explanation
Indices: 3734--4023 Score: 367
Period size: 101 Copynumber: 2.9 Consensus size: 101
3724 ACCGAGAAGC
* * * * * * *
3734 TTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGCCACGTGTG
1 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG--GAATGATGGTCACATGTG
*
3799 TAGTACTATGTGAAGGCTA-T-TACGTGAATCGTAAAA
64 TAGTACTATGTGCAGGCTACTATACGTGAATCGTAAAA
*
3835 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATGGGTCGCATGTGT
1 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT-GGTCACATGTGT
*
3900 AGTACTATGTGCAGGCTACTATACGT-ACT-G-AATAGA
65 AGTACTATGTGCAGGCTACTATACGTGAATCGTAA-A-A
3936 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGGAAATGGTCACATGT
1 TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAT-G--ATGGTCACATGT
*
4000 GTAGTACTACGTGCAGGCTACTAT
63 GTAGTACTATGTGCAGGCTACTAT
4024 GTGAACCGGT
Statistics
Matches: 169, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
99 8 0.05
100 30 0.18
101 92 0.54
102 37 0.22
103 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (101 bp):
TTTGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATGGTCACATGTGTA
GTACTATGTGCAGGCTACTATACGTGAATCGTAAAA
Found at i:4093 original size:42 final size:41
Alignment explanation
Indices: 4046--4189 Score: 137
Period size: 42 Copynumber: 3.7 Consensus size: 41
4036 CCATTGACTA
*
4046 TAAAGGTGGTTGCTAAGTGTTGATTCCACCATATTCTAAATG
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACCATA-TCTAAATG
* *
4088 TAAAGGGGGTTGCTAAGTGATGATTCC-CCGA-ATC---AT-
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACC-ATATCTAAATG
* *
4124 T---GGTGGTTGATAAGTGCTGATTCCACCGTATCTTAAATG
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACCATATC-TAAATG
4163 TGAAAGG-GGTTGCTAAGTGCTGATTCC
1 T-AAAGGTGGTTGCTAAGTGCTGATTCC
4190 CCGATTCATT
Statistics
Matches: 83, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
33 20 0.24
34 5 0.06
36 1 0.01
37 2 0.02
38 2 0.02
39 1 0.01
40 2 0.02
41 3 0.04
42 45 0.54
43 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (41 bp):
TAAAGGTGGTTGCTAAGTGCTGATTCCACCATATCTAAATG
Found at i:4173 original size:75 final size:75
Alignment explanation
Indices: 4050--4226 Score: 259
Period size: 75 Copynumber: 2.4 Consensus size: 75
4040 TGACTATAAA
*
4050 GGTGGTTGCTAAGTGTTGATTCCACCATATTCTAAATGTAAAGGGGGTTGCTAAGTGATGATTCC
1 GGTGGTTGCTAAGTGTTGATTCCACCGTATTCTAAATGTAAAGGGGGTTGCTAAGTGATGATTCC
4115 CCGAATCATT
66 CCGAATCATT
* * *
4125 GGTGGTTGATAAGTGCTGATTCCACCGTA-TCTTAAATGTGAAA-GGGGTTGCTAAGTGCTGATT
1 GGTGGTTGCTAAGTGTTGATTCCACCGTATTC-TAAATGT-AAAGGGGGTTGCTAAGTGATGATT
*
4188 CCCCGATTCATT
64 CCCCGAATCATT
* *
4200 AGTGGTTGCTAAGTGTTGAATCCACCG
1 GGTGGTTGCTAAGTGTTGATTCCACCG
4227 ATAACGGATA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
74 2 0.02
75 86 0.95
76 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (75 bp):
GGTGGTTGCTAAGTGTTGATTCCACCGTATTCTAAATGTAAAGGGGGTTGCTAAGTGATGATTCC
CCGAATCATT
Found at i:5622 original size:2 final size:2
Alignment explanation
Indices: 5615--5651 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5605 TGTTAAGTCT
5615 TA TA TA TA TA TA TA TA TA TA 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 T
5652 GTATTTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7756 original size:17 final size:17
Alignment explanation
Indices: 7734--7767 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7724 TATGTTTTTA
7734 TATGAATGGTTGAGATG
1 TATGAATGGTTGAGATG
*
7751 TATGAATGTTTGAGATG
1 TATGAATGGTTGAGATG
7768 CCAATTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (17 bp):
TATGAATGGTTGAGATG
Done.