Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_132 ID=scaffold_132-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: 11923
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.30
Warning! 300 characters in sequence are not A, C, G, or T
Found at i:1118 original size:132 final size:134
Alignment explanation
Indices: 875--1400 Score: 622
Period size: 132 Copynumber: 4.0 Consensus size: 134
865 AGGATTGATT
* * * * *
875 TCTTCTGTCTATTCCACTACTGCCCAGGGAAGTAGAATTATTGGTTTCAATGTACTCTACTGTAA
1 TCTTCAGTCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * * *
940 CCACAGGGAGGTAAAATCTGCCGTCTTCGATCTGCTTCGCTATCT-ATGTAGGAAGGCAAGATCT
66 CCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCGCTGTCTAATGCAGGAAGGCAAGATCT
*
1004 AAAC
131 AAAA
*
1008 TCTTCAGTCTATTCCACTGCTGCCCAGGGGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAGTCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
1072 CCACAGGGAGGTAAAATCTGCCGTCTTCAATCTGCTTCGCTGTCT-ATGCAGGAAGGCAAGATCT
66 CCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCGCTGTCTAATGCAGGAAGGCAAGATCT
1136 AAAA
131 AAAA
*
1140 TCTTC-GATCTATTCCACTGCTGCCCAGGGAAGTAGAAATT-CTGGCTTCAATGTACTCCACTGC
1 TCTTCAG-TCTATTCCACTGCTGCCCAGGGAAGTAG-AATTACTGGCTTCAATGTACTCCACTGT
* * * * * * ** * * *
1203 AA-CATCAGAGAGGTAAAATTTGTCATCTTTGATCTGCTCCACT-ACTGCT-TAGGGAGACAAGA
64 AACCA-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCGCTGTCTAATGCAGGAAGGCAAGA
*
1265 TCCAAAA
128 TCTAAAA
* * * *
1272 TCCTCAATCTATTCCATTGATGCCCA-GGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
1 TCTTCAGTCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTA
* * ** *
1336 ACCTCATGGAGGTAAAATCCACCATCTTTGATCTGCTCCGCTGT-TAATGCAGGAAGGCAAGATC
65 ACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCGCTGTCTAATGCAGGAAGGCAAGATC
1400 T
130 T
1401 GCTATTTTCA
Statistics
Matches: 336, Mismatches: 46, Indels: 22
0.83 0.11 0.05
Matches are distributed among these distances:
131 10 0.03
132 223 0.66
133 99 0.29
134 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (134 bp):
TCTTCAGTCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCGCTGTCTAATGCAGGAAGGCAAGATCT
AAAA
Found at i:1372 original size:265 final size:265
Alignment explanation
Indices: 882--1400 Score: 688
Period size: 265 Copynumber: 2.0 Consensus size: 265
872 ATTTCTTCTG
* * * * *
882 TCTATTCCACTACTGCCCAGGGAAGTAGAATTATTGGTTTCAATGTACTCTACTGTAACCACAGG
1 TCTATTCCACTACTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCACAGA
* * * * * * *
947 GAGGTAAAATCTGCCGTCTTCGATCTGCTTCGCTATCTATGTAGGAAGGCAAGATCTAAACTCTT
66 GAGGTAAAATCTGCCATCTTCGATCTGCTCCACTATCTATGTAGGAAGACAAGATCCAAAATCCT
* * *
1012 CAGTCTATTCCACTGCTGCCCAGGGGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
131 CAATCTATTCCACTGATGCCCAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
** * *
1077 GGGAGGTAAAATCTGCCGTCTTCAATCTGCTTCGCTGTCT-ATGCAGGAAGGCAAGATCTAAAAT
196 GGGAGGTAAAATCCACCATCTTCAATCTGCTCCGCTGT-TAATGCAGGAAGGCAAGATCTAAAAT
1141 CTTCGA
260 CTTCGA
*
1147 TCTATTCCACTGCTGCCCAGGGAAGTAGAAATT-CTGGCTTCAATGTACTCCACTGCAA-CATCA
1 TCTATTCCACTACTGCCCAGGGAAGTAG-AATTACTGGCTTCAATGTACTCCACTGCAACCA-CA
* * * * *
1210 GAGAGGTAAAATTTGTCATCTTTGATCTGCTCCACTA-CTGCT-TAGGGAGACAAGATCCAAAAT
64 GAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTATCT-ATGTAGGAAGACAAGATCCAAAAT
*
1273 CCTCAATCTATTCCATTGATGCCCAGGAAGATAGAATTACTGGCTTCAATGTACTCCACTGTAAC
128 CCTCAATCTATTCCACTGATGCCCAGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTAAC
* * **
1338 CTCATGGAGGTAAAATCCACCATCTTTGATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCT
192 CACAGGGAGGTAAAATCCACCATCTTCAATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCT
1401 GCTATTTTCA
Statistics
Matches: 219, Mismatches: 30, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
264 45 0.21
265 170 0.78
266 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (265 bp):
TCTATTCCACTACTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGCAACCACAGA
GAGGTAAAATCTGCCATCTTCGATCTGCTCCACTATCTATGTAGGAAGACAAGATCCAAAATCCT
CAATCTATTCCACTGATGCCCAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
GGGAGGTAAAATCCACCATCTTCAATCTGCTCCGCTGTTAATGCAGGAAGGCAAGATCTAAAATC
TTCGA
Found at i:2644 original size:13 final size:14
Alignment explanation
Indices: 2626--2656 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2616 CATTTTTACT
2626 TTTTCATC-TTTCA
1 TTTTCATCTTTTCA
2639 TTTTCATCTTTTCA
1 TTTTCATCTTTTCA
2653 TTTT
1 TTTT
2657 TTCACATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTCATCTTTTCA
Found at i:7303 original size:14 final size:14
Alignment explanation
Indices: 7274--7317 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
7264 AATTTACAGC
*
7274 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
7288 ATTTACAAATATAT
1 ATATACAAATAAAT
7302 ATATACAAATACAAT
1 ATATACAAATA-AAT
7317 A
1 A
7318 CACAAGTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 21 0.88
15 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:7815 original size:3 final size:3
Alignment explanation
Indices: 7802--7837 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
7792 ATATGTATAG
*
7802 ATA AT- ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
7838 ATAGGGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Done.