Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009750.1 Kokia drynarioides strain JFW-HI SEQ_124469, 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: 12610
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:216 original size:13 final size:13
Alignment explanation
Indices: 186--237 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
176 ATCAAGGATG
* *
186 ATAATAAATGACA
1 ATAATAAATAATA
*
199 ATAATAAATATTA
1 ATAATAAATAATA
* *
212 TTAATTAATAATA
1 ATAATAAATAATA
225 ATAAT-AATAATA
1 ATAATAAATAATA
237 A
1 A
238 GTATTTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 8 0.25
13 24 0.75
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:1367 original size:29 final size:29
Alignment explanation
Indices: 1292--1369 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
1282 TTCCTTTAAC
1292 CTCCAAAAATTCCATTTTTGACCCAAAAA
1 CTCCAAAAATTCCATTTTTGACCCAAAAA
** *
1321 CTCTTAAAATTACCATTTTT-ACCCCAAAAT
1 CTCCAAAAATT-CCATTTTTGA-CCCAAAAA
* *
1351 GTCCAAAAATTCTATTTTT
1 CTCCAAAAATTCCATTTTT
1370 TATCCCGATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
CTCCAAAAATTCCATTTTTGACCCAAAAA
Found at i:1499 original size:28 final size:28
Alignment explanation
Indices: 1442--1503 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1432 CCAAATTTTC
* *
1442 CCAAAGTTACCATTTTATCCCCGAGAAT
1 CCAAAATTACCATTTTAGCCCCGAGAAT
* *
1470 CCAAAATTACCATTTT-GCCCTCGGGTAT
1 CCAAAATTACCATTTTAGCCC-CGAGAAT
1498 CCAAAA
1 CCAAAA
1504 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTAGCCCCGAGAAT
Found at i:2450 original size:23 final size:23
Alignment explanation
Indices: 2424--2476 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2414 GTTTTGGTGC
* *
2424 TTTTTTTATTG-TTTTGTTTGTTA
1 TTTTTGTATTGTTTTTG-CTGTTA
*
2447 TTTTCGTATTGTTTTTGCTGTTA
1 TTTTTGTATTGTTTTTGCTGTTA
2470 TTTTTGT
1 TTTTTGT
2477 TGCTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.08, C:0.04, G:0.15, T:0.74
Consensus pattern (23 bp):
TTTTTGTATTGTTTTTGCTGTTA
Found at i:2473 original size:12 final size:12
Alignment explanation
Indices: 2435--2492 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
2425 TTTTTTATTG
2435 TTTTGTTTGTTAT
1 TTTTG-TTGTTAT
* * *
2448 TTTCG-TATTGT
1 TTTTGTTGTTAT
*
2459 TTTTGCTGTTAT
1 TTTTGTTGTTAT
*
2471 TTTTGTTGCTAT
1 TTTTGTTGTTAT
2483 TTTTGTTGTT
1 TTTTGTTGTT
2493 TTTAATGTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.23
12 23 0.66
13 4 0.11
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:2488 original size:44 final size:44
Alignment explanation
Indices: 2440--2529 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 44
2430 TATTGTTTTG
* *
2440 TTTGTTATTTTCGTATTGTT-TTTGCTGTT-ATTTTTGTTGCTATT
1 TTTGTTATTTT--TAATGTTGTTTGCTGTTAATTTTTGCTGCTATT
* *
2484 TTTGTTGTTTTTAATGTTGTTTGCTGTTAATTTTTGCTGCTGTT
1 TTTGTTATTTTTAATGTTGTTTGCTGTTAATTTTTGCTGCTATT
2528 TT
1 TT
2530 GGTTGTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
42 6 0.15
43 9 0.22
44 25 0.62
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.67
Consensus pattern (44 bp):
TTTGTTATTTTTAATGTTGTTTGCTGTTAATTTTTGCTGCTATT
Found at i:2535 original size:44 final size:43
Alignment explanation
Indices: 2456--2550 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
2446 ATTTTCGTAT
* *
2456 TGTT-TTTGCTGTTATTTTTGTTGCTATTTTTGTTGTT-TTTAA
1 TGTTGTTTGCTGTTATTTTTGCTGCTATTTTGGTTGTTATTT-A
* *
2498 TGTTGTTTGCTGTTAATTTTTGCTGCTGTTTTGGTTGTTATTTT
1 TGTTGTTTGCTGTT-ATTTTTGCTGCTATTTTGGTTGTTATTTA
2542 TGTTGTTTG
1 TGTTGTTTG
2551 GATGTTACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 4 0.09
43 9 0.20
44 30 0.65
45 3 0.07
ACGTcount: A:0.07, C:0.05, G:0.21, T:0.66
Consensus pattern (43 bp):
TGTTGTTTGCTGTTATTTTTGCTGCTATTTTGGTTGTTATTTA
Found at i:3143 original size:8 final size:8
Alignment explanation
Indices: 3130--3159 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3120 ATGCAAACTA
*
3130 ATATATAT
1 ATATATAG
3138 ATATATAG
1 ATATATAG
3146 ATATATAG
1 ATATATAG
3154 ATATAT
1 ATATAT
3160 TATTTAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (8 bp):
ATATATAG
Found at i:3539 original size:46 final size:45
Alignment explanation
Indices: 3460--3572 Score: 133
Period size: 46 Copynumber: 2.5 Consensus size: 45
3450 ATATTCTATT
* * **
3460 ATAATATCTCAT-A-ATATCCCATTAGAAATCAAATTGTTAAGAA-
1 ATAATATCTCATAATATATCCTATTAGAAACCAAATTACTAA-AAG
3503 ATAATATCTCATAATTATATCCTATTAGAAACCAAATTACTAAAAG
1 ATAATATCTCATAA-TATATCCTATTAGAAACCAAATTACTAAAAG
*
3549 ATAGTATCTCATAATAATATCCTA
1 ATAATATCTCATAAT-ATATCCTA
3573 GCATTCCCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
43 12 0.20
44 1 0.02
45 3 0.05
46 44 0.73
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (45 bp):
ATAATATCTCATAATATATCCTATTAGAAACCAAATTACTAAAAG
Done.