Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_437 ID=scaffold_437-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: 7104
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:227 original size:108 final size:108
Alignment explanation
Indices: 2--289 Score: 454
Period size: 108 Copynumber: 2.7 Consensus size: 108
1 C
* *
2 TTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTTGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
*
67 CGATTTCTCGTTCGACCAAATAACTTAATATCCTTTTCAAAAA
66 CGATTTCTCGTTCGACCAAATAACTAAATATCCTTTTCAAAAA
* * *
110 TTTTCAAAATAAGGCAATATTTTACGTTTGGAAATTCGAGGAATGTG-CCTAAGGTACTGGGTCT
1 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
*
174 CGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTT-AAAAA
66 CGATTTCTCGTTCGACCAAATAACTAAATATCCTTTTCAAAAA
* * *
216 TTTTTCAAAAATAAGGAAATATTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGT
1 -TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGT
281 TTCGATTTC
64 TTCGATTTC
290 ACGGTTAACC
Statistics
Matches: 164, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
106 5 0.03
107 56 0.34
108 81 0.49
109 22 0.13
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (108 bp):
TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
CGATTTCTCGTTCGACCAAATAACTAAATATCCTTTTCAAAAA
Found at i:3845 original size:8 final size:8
Alignment explanation
Indices: 3832--3899 Score: 86
Period size: 8 Copynumber: 8.4 Consensus size: 8
3822 CAGACTCAAA
3832 AAAAAATC
1 AAAAAATC
3840 AAAAAA-C
1 AAAAAATC
3847 AAAAAATC
1 AAAAAATC
3855 AAAAAAAATC
1 --AAAAAATC
*
3865 AAAAAAATT
1 -AAAAAATC
3874 AAAAAATC
1 AAAAAATC
3882 AAAAAATC
1 AAAAAATC
3890 -AAAAATC
1 AAAAAATC
3897 AAA
1 AAA
3900 GTCAAAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
7 14 0.26
8 24 0.44
9 8 0.15
10 8 0.15
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATC
Found at i:3852 original size:17 final size:18
Alignment explanation
Indices: 3832--3894 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
3822 CAGACTCAAA
3832 AAAAAATC--AAAAAA-C
1 AAAAAATCAAAAAAAATC
3847 AAAAAATCAAAAAAAATC
1 AAAAAATCAAAAAAAATC
*
3865 AAAAAA--ATTAAAAAATC
1 AAAAAATCA-AAAAAAATC
3882 AAAAAATCAAAAA
1 AAAAAATCAAAAA
3895 TCAAAGTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 8 0.20
16 1 0.03
17 20 0.50
18 10 0.25
19 1 0.03
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAATCAAAAAAAATC
Found at i:3864 original size:25 final size:25
Alignment explanation
Indices: 3830--3899 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
3820 TTCAGACTCA
3830 AAAAAAAATCAAAAAACAAAAAATC
1 AAAAAAAATCAAAAAACAAAAAATC
*
3855 AAAAAAAATCAAAAAAATTAAAAAATC
1 AAAAAAAATC-AAAAAA-CAAAAAATC
*
3882 --AAAAAATCAAAAATCAAA
1 AAAAAAAATCAAAAAACAAA
3900 GTCAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.08
24 5 0.12
25 18 0.45
26 6 0.15
27 8 0.20
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.11
Consensus pattern (25 bp):
AAAAAAAATCAAAAAACAAAAAATC
Found at i:4803 original size:13 final size:13
Alignment explanation
Indices: 4794--4823 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4784 AAAAAAATAA
4794 AAAATGAAAAATG
1 AAAATGAAAAATG
*
4807 AGAATGAAAAATG
1 AAAATGAAAAATG
4820 AAAA
1 AAAA
4824 ATGGAGAGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:4806 original size:7 final size:7
Alignment explanation
Indices: 4786--4826 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
4776 AAAAAAATAA
*
4786 AAAAATA
1 AAAAATG
4793 AAAAATG
1 AAAAATG
4800 AAAAATG
1 AAAAATG
*
4807 -AGAATG
1 AAAAATG
4813 AAAAATG
1 AAAAATG
4820 AAAAATG
1 AAAAATG
4827 GAGAGGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:6365 original size:25 final size:25
Alignment explanation
Indices: 6319--6368 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6309 CAGTTAAAAA
* * *
6319 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
6344 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
6369 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:6472 original size:25 final size:25
Alignment explanation
Indices: 6444--6493 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
6434 CAGTTAAAAA
* *
6444 GATTAAAGCCACATCAGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
6469 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
6494 ACGCCCCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:6593 original size:125 final size:125
Alignment explanation
Indices: 6219--6581 Score: 665
Period size: 125 Copynumber: 2.9 Consensus size: 125
6209 CGGTTAAAAA
* * *
6219 GATTAAAGCTACATCAGCAAATCTTAC-CTCTCAAGCGATGCAGTGGAATAGATTAAAGCCAAAT
1 GATTAAAGCTACAACAGCGAATCTTACGC-CCCAAGCGATGCAGTGGAATAGATTAAAGCCAAAT
6283 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
65 TGGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
6344 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATT
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATT
*
6409 GGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCAGTGAATCTT
66 GGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
6469 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATT
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATT
*
6534 GGTGAATCTTGTTTCTCTGACATTGCAGTTAAAAAGATTAAAGCCACA
66 GGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACA
6582 ATGGCGAATC
Statistics
Matches: 232, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
125 231 1.00
126 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (125 bp):
GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATT
GGTGAATCTTGTTTCTCCGACATTGCAGTTAAAAAGATTAAAGCCACATCGGTGAATCTT
Found at i:6966 original size:41 final size:43
Alignment explanation
Indices: 6903--7023 Score: 113
Period size: 46 Copynumber: 2.8 Consensus size: 43
6893 TAAAATAAAT
* * *
6903 GATCTTATCTCTCTGA-AGTTACAGCAGAGTAGAT-CGCA-TCA
1 GATCTTATCTCCCTGAGA-TTACAGCAGAGTAGATAAGAATTCA
* **
6944 GGTCTTATCTCCCTGAGATTACAGTGGAGTAGACTGAAGAATTTCA
1 GATCTTATCTCCCTGAGATTACAGCAGAGTAGA-T-AAGAA-TTCA
* *
6990 GATTTTATCTCCCTGAGATTACAGCAGAGCAGAT
1 GATCTTATCTCCCTGAGATTACAGCAGAGTAGAT
7024 TGAAGTCGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
41 27 0.43
42 2 0.03
44 2 0.03
45 1 0.02
46 31 0.49
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
GATCTTATCTCCCTGAGATTACAGCAGAGTAGATAAGAATTCA
Done.