Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005826.1 Kokia drynarioides strain JFW-HI SEQ_120115, whole genome shotgun sequence
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: 13474
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1170 original size:7 final size:7
Alignment explanation
Indices: 1158--1209 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
1148 TTCAAAAAAA
1158 GTCAACG
1 GTCAACG
1165 GTCAACG
1 GTCAACG
* *
1172 ATTAACG
1 GTCAACG
*
1179 GTCAATG
1 GTCAACG
1186 GTCAACG
1 GTCAACG
*
1193 ATCAACG
1 GTCAACG
1200 GTCAACG
1 GTCAACG
1207 GTC
1 GTC
1210 GATCAATGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1188 original size:21 final size:21
Alignment explanation
Indices: 1158--1209 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1148 TTCAAAAAAA
*
1158 GTCAACGGTCAACGATTAACG
1 GTCAACGGTCAACGATCAACG
*
1179 GTCAATGGTCAACGATCAACG
1 GTCAACGGTCAACGATCAACG
1200 GTCAACGGTC
1 GTCAACGGTC
1210 GATCAATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (21 bp):
GTCAACGGTCAACGATCAACG
Found at i:1273 original size:15 final size:15
Alignment explanation
Indices: 1253--1286 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1243 GGGTTTGGAC
1253 TTGGTTCAATTCGGT
1 TTGGTTCAATTCGGT
*
1268 TTGGTTCAATTGGGT
1 TTGGTTCAATTCGGT
1283 TTGG
1 TTGG
1287 GCTTAATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.32, T:0.47
Consensus pattern (15 bp):
TTGGTTCAATTCGGT
Found at i:3027 original size:30 final size:30
Alignment explanation
Indices: 2991--3158 Score: 121
Period size: 30 Copynumber: 5.7 Consensus size: 30
2981 CCATAGATAT
*
2991 CCACAAAGGCATCTCATATAACTGAATCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
3021 CCACAAAGGC-TCTCATATAACAT-ATTTC-A
1 CCACAAAGGCATCTCATATAAC-TGA-TTCAA
* * *
3050 CCACAAAGGTATCACATATAACAGATTCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
* * ** **
3080 CCACAAAGACTTAACATATAA-TGGATTCTG
1 CCACAAAGGCATCTCATATAACT-GATTCAA
* * * **
3110 CCACAAGGGCATCACTTATAACAAATTCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
* *
3140 CCACATAGGC-TTTCATATA
1 CCACAAAGGCATCTCATATA
3159 TCAAAATTAG
Statistics
Matches: 106, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
29 31 0.29
30 75 0.71
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (30 bp):
CCACAAAGGCATCTCATATAACTGATTCAA
Found at i:3083 original size:59 final size:58
Alignment explanation
Indices: 2991--3158 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 58
2981 CCATAGATAT
* * * *
2991 CCACAAAGGCATCTCATATAACTGAATCAACCACAAAGGCTCTCATATAACATATT-TCA
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCT-TCATATAACAGATTCT-A
* * ** *
3050 CCACAAAGGTATCACATATAACAGATTCAACCACAAAGACTTAACATATAATGGATTCTG
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCTT--CATATAACAGATTCTA
* * * *
3110 CCACAAGGGCATCACTTATAACAAATTCAACCACATAGGCTTTCATATA
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGC-TTCATATA
3159 TCAAAATTAG
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 1 0.01
59 42 0.47
60 44 0.49
61 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (58 bp):
CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCTTCATATAACAGATTCTA
Found at i:3163 original size:29 final size:28
Alignment explanation
Indices: 3126--3185 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3116 GGGCATCACT
*
3126 TATAAC-AAATTCAACCACATAGGCTTTCA
1 TATAACAAAATT-AACCACAAAGGC-TTCA
* *
3155 TATATCAAAATTAGCCACAAAGGCTTCA
1 TATAACAAAATTAACCACAAAGGCTTCA
3183 TAT
1 TAT
3186 CGGTAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 15 0.56
30 5 0.19
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (28 bp):
TATAACAAAATTAACCACAAAGGCTTCA
Found at i:5617 original size:12 final size:12
Alignment explanation
Indices: 5600--5628 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5590 TTATTAATTC
5600 TATTTATTTTAA
1 TATTTATTTTAA
5612 TATTTATTTTAA
1 TATTTATTTTAA
5624 TATTT
1 TATTT
5629 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:8608 original size:20 final size:20
Alignment explanation
Indices: 8560--8614 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
8550 TTATTTAAAA
* *
8560 CCCTGTATGCACTTCGATGC
1 CCCTGTATGCACTACGATAC
* * *
8580 CTCTATATGCACTACGGTAC
1 CCCTGTATGCACTACGATAC
8600 CCCTGTATGCACTAC
1 CCCTGTATGCACTAC
8615 AATGCCCTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (20 bp):
CCCTGTATGCACTACGATAC
Found at i:11108 original size:29 final size:29
Alignment explanation
Indices: 11075--11134 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
11065 TAGGAATAGG
*
11075 AAATTCCATTAGGATATCTTAGGTTAATT
1 AAATTCCATTAGGATATCTTAAGTTAATT
* * *
11104 AAATTCCATTAGGTTCTTTTAAGTTAATT
1 AAATTCCATTAGGATATCTTAAGTTAATT
11133 AA
1 AA
11135 TTTAATTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (29 bp):
AAATTCCATTAGGATATCTTAAGTTAATT
Found at i:11539 original size:15 final size:15
Alignment explanation
Indices: 11519--11547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11509 GTGTGTTAAC
11519 TTTTAATTATTTTTA
1 TTTTAATTATTTTTA
11534 TTTTAATTATTTTT
1 TTTTAATTATTTTT
11548 GTTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTATTTTTA
Found at i:11543 original size:9 final size:9
Alignment explanation
Indices: 11519--11573 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
11509 GTGTGTTAAC
11519 TTTTAATTA
1 TTTTAATTA
11528 -TTT--TTA
1 TTTTAATTA
11534 TTTTAATTA
1 TTTTAATTA
**
11543 TTTTTGTTA
1 TTTTAATTA
11552 TTTTTAATTA
1 -TTTTAATTA
11562 -TTTAATTA
1 TTTTAATTA
11570 TTTT
1 TTTT
11574 TAGATACCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 11 0.30
9 13 0.35
10 7 0.19
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTAATTA
Found at i:13343 original size:17 final size:17
Alignment explanation
Indices: 13318--13351 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13308 AAATCACCTC
*
13318 AATACCATATTATGCAA
1 AATACCATAATATGCAA
*
13335 AATATCATAATATGCAA
1 AATACCATAATATGCAA
13352 TAATTAAACT
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:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
AATACCATAATATGCAA
Done.