Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_519 ID=scaffold_519-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: 6125
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Found at i:1093 original size:10 final size:10
Alignment explanation
Indices: 1070--1152 Score: 57
Period size: 10 Copynumber: 8.4 Consensus size: 10
1060 CTAATTCAAA
*
1070 TTTTTATGATT
1 TTTTTAT-AAT
1081 TTTTTATAA-
1 TTTTTATAAT
*
1090 TTTTTATAAG
1 TTTTTATAAT
*
1100 TTTATATCAA-
1 TTTTTAT-AAT
* *
1110 TTTTAATATT
1 TTTTTATAAT
1120 TTTTTCAT-AT
1 TTTTT-ATAAT
*
1130 TTTTTACAAT
1 TTTTTATAAT
1140 TTTTT-TAAT
1 TTTTTATAAT
1149 TTTT
1 TTTT
1153 AAAGTAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
9 18 0.31
10 29 0.50
11 11 0.19
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1093 original size:20 final size:19
Alignment explanation
Indices: 1068--1153 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
1058 GTCTAATTCA
1068 AATTTTTATGATTTTTTTAT
1 AATTTTTAT-ATTTTTTTAT
** *
1088 AATTTTTATAAGTTTATAT
1 AATTTTTATATTTTTTTAT
*
1107 CAATTTTAATATTTTTTTCAT
1 -AATTTTTATATTTTTTT-AT
* * *
1128 ATTTTTTACAATTTTTT-T
1 AATTTTTATATTTTTTTAT
1146 AATTTTTA
1 AATTTTTA
1154 AAGTAATATA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
18 8 0.15
19 7 0.13
20 35 0.67
21 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.65
Consensus pattern (19 bp):
AATTTTTATATTTTTTTAT
Found at i:1235 original size:10 final size:9
Alignment explanation
Indices: 1081--1236 Score: 79
Period size: 9 Copynumber: 17.0 Consensus size: 9
1071 TTTTATGATT
1081 TTTTTATAA
1 TTTTTATAA
1090 TTTTTATAA
1 TTTTTATAA
*
1099 GTTTATATCAA
1 -TTTTTAT-AA
* *
1110 TTTTAATATT
1 TTTTTATA-A
*
1120 TTTTTCATAT
1 TTTTT-ATAA
*
1130 TTTTTACAA
1 TTTTTATAA
*
1139 TTTTTTTAA
1 TTTTTATAA
1148 TTTTTA-AA
1 TTTTTATAA
* **
1156 GTAATAT-A
1 TTTTTATAA
1164 TTTTT-TAA
1 TTTTTATAA
**
1172 TTTAAAT-A
1 TTTTTATAA
**
1180 TTGTAAATAA
1 TT-TTTATAA
1190 TTTTTATTAA
1 TTTTTA-TAA
1200 TTTATTAT-A
1 TTT-TTATAA
1209 TTTTTATAA
1 TTTTTATAA
*
1218 TATTTATAA
1 TTTTTATAA
1227 GTTTTTATAA
1 -TTTTTATAA
1237 AAAAGAAATT
Statistics
Matches: 112, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
7 1 0.01
8 19 0.17
9 45 0.40
10 39 0.35
11 8 0.07
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:2233 original size:3 final size:3
Alignment explanation
Indices: 2225--2316 Score: 87
Period size: 3 Copynumber: 30.7 Consensus size: 3
2215 AAAACAACCA
* * * * *
2225 CTG CTG CTG CTG CTG CCG CCG CCT- CTG CTG CTG CTG CCG CCG CCG
1 CTG CTG CTG CTG CTG CTG CTG -CTG CTG CTG CTG CTG CTG CTG CTG
* * * *
2270 CCG CCG CCG CTG CTG CTG CTG CCG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
2317 ATAATCCAAG
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.02
3 78 0.96
4 1 0.01
ACGTcount: A:0.00, C:0.45, G:0.32, T:0.24
Consensus pattern (3 bp):
CTG
Found at i:3196 original size:22 final size:23
Alignment explanation
Indices: 3171--3220 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
3161 AATTTTAATT
3171 TTTTATGATTCAAA-AATA-AATA
1 TTTTAT-ATTCAAATAATAGAATA
*
3193 TTTTATATTTAAATAATAGAATA
1 TTTTATATTCAAATAATAGAATA
*
3216 ATTTA
1 TTTTA
3221 AAAACTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 10 0.42
23 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTTATATTCAAATAATAGAATA
Found at i:3558 original size:20 final size:19
Alignment explanation
Indices: 3524--3564 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3514 AAATTATTTT
*
3524 AAAATTTATAAAAATAGAA
1 AAAATTTAAAAAAATAGAA
*
3543 AAAATATTAAAAAAATATAA
1 AAAAT-TTAAAAAAATAGAA
3563 AA
1 AA
3565 TTAATTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATTTAAAAAAATAGAA
Found at i:4958 original size:17 final size:17
Alignment explanation
Indices: 4925--4958 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4915 TTTTATTTAT
* *
4925 CAAAATAATACAAAAAA
1 CAAAAAAATAAAAAAAA
4942 CAAAAAAATAAAAAAAA
1 CAAAAAAATAAAAAAAA
4959 GTTACTGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (17 bp):
CAAAAAAATAAAAAAAA
Found at i:5091 original size:20 final size:20
Alignment explanation
Indices: 5068--5131 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
5058 AAAGGAGAGG
5068 GAAAGGAGAAAAAAGAAAGA
1 GAAAGGAGAAAAAAGAAAGA
*
5088 GAAA-AAGAAAGAAAGAAA-A
1 GAAAGGAGAAA-AAAGAAAGA
*
5107 GGAAAGGAGGAAAAAGAAAGA
1 -GAAAGGAGAAAAAAGAAAGA
5128 GAAA
1 GAAA
5132 AAGAAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 6 0.16
20 26 0.70
21 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAGGAGAAAAAAGAAAGA
Found at i:5093 original size:14 final size:14
Alignment explanation
Indices: 5076--5140 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
5066 GGGAAAGGAG
5076 AAAAAAGAAAGAG-
1 AAAAAAGAAAGAGA
5089 -AAAAAGAAAGA-A
1 AAAAAAGAAAGAGA
*
5101 AGAAAAGGAAAG-GA
1 A-AAAAAGAAAGAGA
*
5115 GGAAAAAGAAAGAGA
1 -AAAAAAGAAAGAGA
5130 AAAAGAAGAAA
1 AAAA-AAGAAA
5141 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 11 0.27
14 22 0.54
15 8 0.20
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAGAGA
Found at i:5141 original size:20 final size:19
Alignment explanation
Indices: 5074--5141 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
5064 GAGGGAAAGG
5074 AGAAAAAAGAAAGAGAAAA
1 AGAAAAAAGAAAGAGAAAA
*
5093 AGAAAGAAAGAAA-AGGAAAGG
1 AGAAA-AAAGAAAGA-GAAA-A
*
5114 AGGAAAAAGAAAGAGAAAA
1 AGAAAAAAGAAAGAGAAAA
5133 AGAAGAAAA
1 AGAA-AAAA
5142 TGTAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 9 0.22
20 26 0.65
21 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AGAAAAAAGAAAGAGAAAA
Done.