Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_587 ID=scaffold_587-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: 5555
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:1632 original size:19 final size:19
Alignment explanation
Indices: 1608--1654 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1598 ACGTCTCTTT
*
1608 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
1627 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
1646 TATGCATTA
1 TTTGCATTA
1655 GATTTTCCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:2961 original size:15 final size:15
Alignment explanation
Indices: 2941--2990 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
2931 CAGACTCAAA
*
2941 AAAAAATCAAAAATT
1 AAAAAATCAAAAATC
2956 AAAAAATCAAAAATC
1 AAAAAATCAAAAATC
*
2971 AAAAAAAT-AAAAGTC
1 -AAAAAATCAAAAATC
2986 AAAAA
1 AAAAA
2991 TAGGAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 5 0.16
15 20 0.62
16 7 0.22
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (15 bp):
AAAAAATCAAAAATC
Found at i:2968 original size:22 final size:22
Alignment explanation
Indices: 2942--2991 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2932 AGACTCAAAA
2942 AAAAATCAAAAATTAA-AAAA-TC
1 AAAAATCAAAAA--AATAAAAGTC
2964 AAAAATCAAAAAAATAAAAGTC
1 AAAAATCAAAAAAATAAAAGTC
2986 AAAAAT
1 AAAAAT
2992 AGGAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.08
21 4 0.15
22 20 0.77
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAATCAAAAAAATAAAAGTC
Found at i:2990 original size:8 final size:7
Alignment explanation
Indices: 2942--2975 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2932 AGACTCAAAA
2942 AAAAATC
1 AAAAATC
*
2949 AAAAATTA
1 AAAAA-TC
2957 AAAAATC
1 AAAAATC
2964 AAAAATC
1 AAAAATC
2971 AAAAA
1 AAAAA
2976 AATAAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATC
Found at i:3003 original size:14 final size:14
Alignment explanation
Indices: 2995--3043 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2985 CAAAAATAGG
2995 AGAAAAAAAAGAGA
1 AGAAAAAAAAGAGA
3009 AGAAAAAAAAGA-A
1 AGAAAAAAAAGAGA
*
3022 A-AAAGAAAAAGAAAA
1 AGAAA-AAAAAG-AGA
3037 AGAAAAA
1 AGAAAAA
3044 GAAAAAGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.10
13 8 0.26
14 13 0.42
15 4 0.13
16 3 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAGAGA
Found at i:3028 original size:19 final size:20
Alignment explanation
Indices: 3000--3049 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
2990 ATAGGAGAAA
3000 AAAAAGAGAAGAAA-AAAAAG
1 AAAAAGAGAA-AAAGAAAAAG
3020 AAAAA-AGAAAAAGAAAAAG
1 AAAAAGAGAAAAAGAAAAAG
3039 AAAAAGA-AAAA
1 AAAAAGAGAAAA
3050 GGAGAGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.11
19 19 0.68
20 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAGAGAAAAAGAAAAAG
Found at i:3030 original size:6 final size:6
Alignment explanation
Indices: 2995--3050 Score: 71
Period size: 6 Copynumber: 9.3 Consensus size: 6
2985 CAAAAATAGG
*
2995 AGAAAA A-AAAG AGAAGAA A-AAAA AGAAAAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAA-AA AGAAAA AG-AAAA AGAAAA AGAAAA AGAAAA
3043 AGAAAA AG
1 AGAAAA AG
3051 GAGAGGTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 7 0.16
6 29 0.66
7 8 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:3956 original size:10 final size:10
Alignment explanation
Indices: 3929--3965 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
3919 GAGTCAAACA
3929 AAAAAAAATG
1 AAAAAAAATG
3939 AATGAAAAAATG
1 AA--AAAAAATG
3951 AAAAAAAATG
1 AAAAAAAATG
3961 AAAAA
1 AAAAA
3966 GTAAAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:5316 original size:44 final size:43
Alignment explanation
Indices: 5180--5318 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 43
5170 GACAATAGAT
*
5180 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCT-CATTGACAGCGAAGCAGGTCGAAGACACAAAC
* * ** * * * *
5224 ATTGCC-TCTCTCGGTTGTGATG-G-AGCTGGTTGAAGACAAAAGAT
1 CTTGCCTTC-CTC-ATTGACA-GCGAAGCAGGTCGAAGACACAA-AC
*
5268 CTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGACACAAAC
1 CTTGCCTTCCT-CATTGACAGCGAAGCAGGTCGAAGACACAAAC
5312 CTTGCCT
1 CTTGCCT
5319 CCATCGGTTG
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
43 18 0.26
44 33 0.48
45 18 0.26
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (43 bp):
CTTGCCTTCCTCATTGACAGCGAAGCAGGTCGAAGACACAAAC
Found at i:5317 original size:88 final size:88
Alignment explanation
Indices: 5166--5328 Score: 265
Period size: 88 Copynumber: 1.9 Consensus size: 88
5156 AACAGATCAG
* ** *
5166 TGAAGACAATAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACATTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGACACAAACATTGCCT
5231 CTC-TCGGTTGTGATGGAGCTGGT
66 C-CATCGGTTGTGATGGAGCTGGT
*
5254 TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGACACAAACATTGCCT
5319 CCATCGGTTG
66 CCATCGGTTG
5329 CAGTGGAGCT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
87 1 0.01
88 68 0.99
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAACAGGTCGAAGACACAAACATTGCCT
CCATCGGTTGTGATGGAGCTGGT
Done.