Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_566 ID=scaffold_566-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: 5646
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Found at i:1071 original size:17 final size:17
Alignment explanation
Indices: 1051--1109 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
1041 TTAATAGATA
1051 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
1068 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
1087 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
1105 ATTGA
1 ATTGA
1110 GTTATGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:1079 original size:37 final size:37
Alignment explanation
Indices: 1038--1112 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1028 AATTAATGAA
1038 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
1075 TGATTAATAGATAATTGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1112 T
1 T
1113 ATGAAATGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:1091 original size:20 final size:19
Alignment explanation
Indices: 1038--1097 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
1028 AATTAATGAA
1038 TGATTAATAGATAATTGAAG
1 TGATTAATAGATAATTG-AG
*
1058 TGAAT-AT-GAT-ATTGAG
1 TGATTAATAGATAATTGAG
1074 TTGATTAATAGATAATTGAAG
1 -TGATTAATAGATAATTG-AG
1095 TGA
1 TGA
1098 ATGTGATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 5 0.15
19 5 0.15
20 11 0.33
21 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TGATTAATAGATAATTGAG
Found at i:1125 original size:20 final size:21
Alignment explanation
Indices: 1097--1141 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1087 AATTGAAGTG
* *
1097 AATGTGATATTGAG-TTATGA
1 AATGCGATATGGAGATTATGA
1117 AATGCGATATGGAGATTATGA
1 AATGCGATATGGAGATTATGA
1138 AATG
1 AATG
1142 TCATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (21 bp):
AATGCGATATGGAGATTATGA
Found at i:1344 original size:75 final size:75
Alignment explanation
Indices: 1219--1389 Score: 213
Period size: 75 Copynumber: 2.3 Consensus size: 75
1209 ATCGCTGTTC
* *
1219 ATCCAACTAGAGCTGGGCTCACAATTATAATCGTTGATATACTCAGCTAGCACTAGGTGCAAATA
1 ATCCAACTAGAGCTGGGCTCACAATTATAATCGTAGATATACTCAGCTAGCACTAGGCGCAAATA
1284 TCATTGGTTT
66 TCATTGGTTT
* * * * *
1294 ATCCAACTAGAGCTGGGCTCACTATT-TATATCGTCAG-TTTA-TCCGACTAGCGCTGGGCGCAA
1 ATCCAACTAGAGCTGGGCTCACAATTATA-ATCGT-AGATATACTCAG-CTAGCACTAGGCGCAA
1356 ATATCATTGGTTT
63 ATATCATTGGTTT
* *
1369 ATCCAACCAGAGTTGGGCTCA
1 ATCCAACTAGAGCTGGGCTCA
1390 TTGATTATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
74 5 0.06
75 78 0.93
76 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (75 bp):
ATCCAACTAGAGCTGGGCTCACAATTATAATCGTAGATATACTCAGCTAGCACTAGGCGCAAATA
TCATTGGTTT
Found at i:1369 original size:35 final size:35
Alignment explanation
Indices: 1277--1386 Score: 103
Period size: 40 Copynumber: 3.0 Consensus size: 35
1267 AGCACTAGGT
1277 GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
1 GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
* * ** * *
1312 TCACTATTTATATCGTCAGTTTATCCGACTAGCGCTGGGC
1 GCA--A---ATATCATTGGTTTATCCAACTAGAGCTGGGC
* *
1352 GCAAATATCATTGGTTTATCCAACCAGAGTTGGGC
1 GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
1387 TCATTGATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
35 26 0.46
37 1 0.02
38 1 0.02
40 28 0.50
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (35 bp):
GCAAATATCATTGGTTTATCCAACTAGAGCTGGGC
Found at i:2714 original size:69 final size:69
Alignment explanation
Indices: 2603--2741 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
2593 AGCCACACGA
* *
2603 CCGTGTGAATCCTGTAGTAAAATTTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
1 CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
2668 GTCC
66 GTCC
2672 CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
1 CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
2737 GTCC
66 GTCC
2741 C
1 C
2742 AAAGTGTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.43
Consensus pattern (69 bp):
CCGTGTGAACCCTGTAGTAAAAATTTTTGCAAATTCTTCTTTAACTTTTCAAATGATTTCTATTA
GTCC
Done.