Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_218 ID=scaffold_218-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: 9231
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Found at i:1656 original size:46 final size:46
Alignment explanation
Indices: 1574--2441 Score: 1244
Period size: 46 Copynumber: 18.9 Consensus size: 46
1564 AAGACTAGTT
* * *
1574 TCTTCGATGTACTCCGCTTCCAAA-ACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
1619 TCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
1665 TCTTCGATCTCCTCCACTGCCAAATACAGGAAGACAAGATCTGCCA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * * *
1711 TCTTTC-ATCTGCT-CGACTGTC-AGTACAGGAAGGCAAGA-CTAG-TT
1 TC-TTCGATCTCCTCCG-CTGCCAAATACAGGAAGACAAGATCT-GCTA
*
1755 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
1801 TCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGACCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
1847 TCTTCGATCTTCTCCGCTGCTAAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
1893 TCTTCGATCTACTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
1939 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGATA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * *
1985 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGTTG
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
2031 CCTTCAATCTCCTCCGCTGCCAAATACAGAAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
2077 TCTTCGATCTCCTCCGCTGTCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * *
2123 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGATAAGATCTGTTG
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * * *
2169 CCTTCAATCTTCTCCGCTGCCAAATACAGAAAGACAAGATTTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
2215 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
*
2261 TCTTCGATCTCCTCTGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* * * * *
2307 TCTTCGATCTCTTCTGCTACCAAATATAGGAAGACAAGATCTGCTG
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
2353 TCTTCGATCTACTCTGCTGCCAAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
* *
2399 TCTTCGATCTACTCCACTGCCAAATACAGGAAGACAAGATCTG
1 TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTG
2442 TTGCTTCTAG
Statistics
Matches: 740, Mismatches: 74, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
43 3 0.00
44 14 0.02
45 55 0.07
46 665 0.90
47 3 0.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (46 bp):
TCTTCGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTGCTA
Found at i:3886 original size:8 final size:8
Alignment explanation
Indices: 3864--3923 Score: 74
Period size: 8 Copynumber: 7.9 Consensus size: 8
3854 CCTCTCCTTT
3864 TTCTTTTC
1 TTCTTTTC
3872 -T-TTTTC
1 TTCTTTTC
3878 TTCTTTTC
1 TTCTTTTC
3886 TT-TTTTC
1 TTCTTTTC
*
3893 TTCTTTTT
1 TTCTTTTC
3901 TTCTTTT-
1 TTCTTTTC
3908 TTCCTTTTC
1 TT-CTTTTC
3917 TTCTTTT
1 TTCTTTT
3924 TGTTTCTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
6 5 0.11
7 11 0.24
8 28 0.61
9 2 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTCTTTTC
Found at i:3901 original size:26 final size:25
Alignment explanation
Indices: 3861--3942 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
3851 TGGCCTCTCC
3861 TTTTTCTTTTCTTTTTCTTCTTTTCT
1 TTTTTCTTTT-TTTTTCTTCTTTTCT
3887 TTTTTCTTCTTTTTTTCTT-TTTTCCT
1 TTTTTCTT-TTTTTTTCTTCTTTT-CT
*
3913 TTTCTTCTTTTTGTTTCTTCTTTT-T
1 TTT-TTCTTTTTTTTTCTTCTTTTCT
3938 TTTTT
1 TTTTT
3943 GAATATTCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
24 2 0.04
25 8 0.16
26 30 0.59
27 11 0.22
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (25 bp):
TTTTTCTTTTTTTTTCTTCTTTTCT
Found at i:3931 original size:34 final size:33
Alignment explanation
Indices: 3864--3943 Score: 53
Period size: 34 Copynumber: 2.4 Consensus size: 33
3854 CCTCTCCTTT
3864 TTCTTTTCTTTTT-CTTCTT-TTCTT-TTTTCTTC
1 TTCTTTTCTTTTTGCTTCTTCTT-TTCTTTT-TTC
* *
3896 TTTTTTTCTTTTTTCCTT-TTCTTCTT-TTTGTTTC
1 TTCTTTTC-TTTTTGCTTCTTCTT-TTCTTT-TTTC
*
3930 TTCTTTTTTTTTTG
1 TTCTTTTCTTTTTG
3944 AATATTCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 7 0.17
33 12 0.30
34 20 0.50
35 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (33 bp):
TTCTTTTCTTTTTGCTTCTTCTTTTCTTTTTTC
Found at i:3938 original size:15 final size:14
Alignment explanation
Indices: 3864--3942 Score: 78
Period size: 13 Copynumber: 5.9 Consensus size: 14
3854 CCTCTCCTTT
*
3864 TTCTTTTCTTTTTC
1 TTCTTTTTTTTTTC
3878 TTCTTTTCTTTTTTC
1 TTCTTTT-TTTTTTC
3893 TTC---TTTTTTTC
1 TTCTTTTTTTTTTC
**
3904 TT-TTTTCCTTTTC
1 TTCTTTTTTTTTTC
*
3917 TTC-TTTTTGTTTC
1 TTCTTTTTTTTTTC
3930 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
3943 GAATATTCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
11 9 0.17
12 1 0.02
13 18 0.35
14 15 0.29
15 9 0.17
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (14 bp):
TTCTTTTTTTTTTC
Found at i:3941 original size:39 final size:39
Alignment explanation
Indices: 3867--3939 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 39
3857 CTCCTTTTTC
*
3867 TTTTCTTTTTCTTCTTTTCTTTTTTCTTCTTTTTTTCTT
1 TTTTCCTTTTCTTCTTTTCTTTTTTCTTCTTTTTTTCTT
*
3906 TTTTCCTTTTCTTC-TTT-TTGTTTCTTCTTTTTTT
1 TTTTCCTTTTCTTCTTTTCTTTTTTCTTCTTTTTTT
3940 TTTGAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 16 0.50
38 3 0.09
39 13 0.41
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (39 bp):
TTTTCCTTTTCTTCTTTTCTTTTTTCTTCTTTTTTTCTT
Done.