Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_192 ID=scaffold_192-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: 9618
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:767 original size:14 final size:14
Alignment explanation
Indices: 738--783 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
728 AATTTACAAC
*
738 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
752 ATTTACAAATACAT
1 ATATACAAATAAAT
766 ATATACAAATATAAT
1 ATATACAAATA-AAT
781 ATA
1 ATA
784 ACAGTAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:1150 original size:2 final size:2
Alignment explanation
Indices: 1143--1167 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1133 GTACATGTAT
1143 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 T
1168 TTAAGTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3033 original size:45 final size:45
Alignment explanation
Indices: 2969--3243 Score: 217
Period size: 44 Copynumber: 6.2 Consensus size: 45
2959 AAGACTCGTA
* *
2969 TCTTCGATCTACTTCACCACCAGTATGGGACGACAAGATCTACTT
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTT
* * *
3014 TCTTCGATCTACTTCACCACCAGTATGGAAAGATAAGATCT-GTA
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTT
* * * * * * *
3058 TATTCGATCCACTTCGCTACC-GATATAGGAAGGCAGGA-C-ATGTT
1 TCTTCGATCTACTTCACCACCAG-TATGGGAAGACAAGATCTA-GTT
* * * ***
3102 ATCTTTGATCTACTTCA-CGCCAATACATGAAGACAAGATCTA-TT
1 -TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTT
* *
3146 TCATTCGATCTACTGCACCACCAGTATGGGGAGACAAGATCT-GTT
1 TC-TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTT
* *** *
3191 TCTTTGATCTACTTCA-CACCAGTACATGAAGATAAGATCT-GTTT
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAG-TT
3235 TCTTCGATC
1 TCTTCGATC
3244 GATTCCACTG
Statistics
Matches: 177, Mismatches: 42, Indels: 23
0.73 0.17 0.10
Matches are distributed among these distances:
43 24 0.14
44 79 0.45
45 73 0.41
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTAGTT
Found at i:3428 original size:132 final size:132
Alignment explanation
Indices: 3267--3737 Score: 648
Period size: 132 Copynumber: 3.6 Consensus size: 132
3257 ACTGGGGAGA
* * * * ** * *
3267 TAGAATTGCTGGCTTTAATATACTCCACTGCAACTTCAGGGAGGTAAAA-TCTGCCGTCTTTGAT
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-ACCATCTTTGAT
*
3331 CTGCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTATTCCGCTGCTGCCCAGGG
65 CTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGG
3396 -AG
130 AAG
* *
3398 ATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA-TCTGCCATCTTTGA
1 -TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-ACCATCTTTGA
* *
3462 TCTGCTTCGCTGTCTA-TGC--AGGAAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCC
64 TCTGC-TC-C--ACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCC
3524 CAGGGAAG
125 CAGGGAAG
* *
3532 TAGAATTACTGGTTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATC
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATC
* * * * *
3597 TGCTCCACTACTGCTTGGGGAGTCAAGATCTAAAATCTTCAATCTATTCCACTGCTGACCAGGGA
66 TGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGA
3662 AG
131 AG
*
3664 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATTCACCATCTTTGATC
1 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATC
3729 TGCTCCACT
66 TGCTCCACT
3738 GTCTATACAG
Statistics
Matches: 305, Mismatches: 25, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
129 3 0.01
130 3 0.01
131 1 0.00
132 178 0.58
133 109 0.36
134 5 0.02
135 3 0.01
136 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATC
TGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGA
AG
Found at i:3697 original size:265 final size:265
Alignment explanation
Indices: 3267--3771 Score: 764
Period size: 265 Copynumber: 1.9 Consensus size: 265
3257 ACTGGGGAGA
* ** * *
3267 TAGAATTGCTGGCTTTAATATACTCCACTGCAACTTCAGGGAGGTAAAATCTGCCGTCTTTGATC
1 TAGAATTACTGGCTTTAATATACTCCACTGCAACCACAGGGAGGTAAAATCTACCATCTTTGATC
** * *
3332 TGCTCCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTATTCCGCTGCTGCCCAGGGA
66 TGCTCCACTACTGCTTAGGGAGGCAAGATCTAAAATCTTCAATCTATTCCACTGCTGACCAGGGA
*
3397 GATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA-TCTGCCATCTTTG
131 GATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-ACCATCTTTG
* * *
3461 ATCTGCTTCGCTGTCTATGCAGGAAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
195 ATCTGCTCCACTGTCTATACAGGAAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
3526 GGGAAG
260 GGGAAG
* * *
3532 TAGAATTACTGGTTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGAT
1 TAGAATTACTGGCTTTAATATACTCCACTGCAACCACAGGGAGGTAAAATCT-ACCATCTTTGAT
* *
3596 CTGCTCCACTACTGCTTGGGGAGTCAAGATCTAAAATCTTCAATCTATTCCACTGCTGACCAGGG
65 CTGCTCCACTACTGCTTAGGGAGGCAAGATCTAAAATCTTCAATCTATTCCACTGCTGACCAGGG
* *
3661 A-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATTCACCATCTTT
130 AGA-TAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTT
**
3725 GATCTGCTCCACTGTCTATACAGGAAGGCAAGATCTGCTATCTTCAA
194 GATCTGCTCCACTGTCTATACAGGAAGGCAAGATCTGAAATCTTCAA
3772 CCTGCTCCAC
Statistics
Matches: 215, Mismatches: 22, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
264 2 0.01
265 211 0.98
266 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (265 bp):
TAGAATTACTGGCTTTAATATACTCCACTGCAACCACAGGGAGGTAAAATCTACCATCTTTGATC
TGCTCCACTACTGCTTAGGGAGGCAAGATCTAAAATCTTCAATCTATTCCACTGCTGACCAGGGA
GATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGA
TCTGCTCCACTGTCTATACAGGAAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAG
GGAAG
Found at i:3768 original size:45 final size:44
Alignment explanation
Indices: 3719--3854 Score: 123
Period size: 45 Copynumber: 3.1 Consensus size: 44
3709 AAAATTCACC
*
3719 ATCTTTGATCTGCTCCACTGTCTATACAGGAAGGCAAGATCTGCT
1 ATCTTCGATCTGCTCCACTGTC-ATACAGGAAGGCAAGATCTGCT
* * * * * * *
3764 ATCTTCAACCTGCTCCACTGTC-TCCGAGGGAGGCGAGGT-TGGT
1 ATCTTCGATCTGCTCCACTGTCATAC-AGGAAGGCAAGATCTGCT
* * * *
3807 GTCTTCGATCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTT
1 ATCTTCGATCTGCTCCACTGTC-ATACAGGAAGGCAAGATCTGCT
3852 ATC
1 ATC
3855 ATCACTAATC
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
43 23 0.33
44 20 0.29
45 26 0.38
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.29
Consensus pattern (44 bp):
ATCTTCGATCTGCTCCACTGTCATACAGGAAGGCAAGATCTGCT
Found at i:9151 original size:14 final size:14
Alignment explanation
Indices: 9122--9167 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
9112 AATTTACAAC
* *
9122 ATATACGAATAAAT
1 ATATACAAATACAT
*
9136 ATTTACAAATACAT
1 ATATACAAATACAT
9150 ATATACAAATACA-
1 ATATACAAATACAT
9163 ATATA
1 ATATA
9168 ACAGTAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATACAAATACAT
Done.