Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009764.1 Kokia drynarioides strain JFW-HI SEQ_124483, 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: 22368
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:107 original size:4 final size:4
Alignment explanation
Indices: 98--150 Score: 61
Period size: 4 Copynumber: 12.8 Consensus size: 4
88 TCTCTCCTTC
* * *
98 TTCT TTCT TTCCT CTCC TTCT TCCT TTCT TTCT TTCT TTCCT TTCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT
148 TTC
1 TTC
151 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 34 0.83
5 7 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTCT
Found at i:138 original size:17 final size:17
Alignment explanation
Indices: 118--150 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
108 CCTCTCCTTC
118 TTCCTTTCTTTCTTTCT
1 TTCCTTTCTTTCTTTCT
135 TTCCTTTCTTTCTTTC
1 TTCCTTTCTTTCTTTC
151 CCGTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTTTCTTTCTTTCT
Found at i:2461 original size:25 final size:23
Alignment explanation
Indices: 2430--2534 Score: 149
Period size: 23 Copynumber: 4.5 Consensus size: 23
2420 AGTGCTGGGC
2430 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
2453 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
2476 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
2500 TAACAGAGAGCACGAGA-AGTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
2524 AACAGAGAGCA
1 AACAGAGAGCA
2535 TGCTAGTGTT
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
23 53 0.72
24 2 0.03
25 17 0.23
26 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:2492 original size:48 final size:48
Alignment explanation
Indices: 2430--2534 Score: 162
Period size: 48 Copynumber: 2.2 Consensus size: 48
2420 AGTGCTGGGC
2430 AACAGAGAGCACACACAGTGCT-A-AACAGAGAGCAC-ACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-AAAGTGCTA
* *
2476 ATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGAAGTGCTA
1 AACAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAAAAGTGCTA
2524 AACAGAGAGCA
1 AACAGAGAGCA
2535 TGCTAGTGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 21 0.40
47 1 0.02
48 30 0.57
49 1 0.02
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.10
Consensus pattern (48 bp):
AACAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAAAAGTGCTA
Found at i:4280 original size:27 final size:26
Alignment explanation
Indices: 4250--4307 Score: 107
Period size: 27 Copynumber: 2.2 Consensus size: 26
4240 AGAAGAGAGG
4250 TGTGTGAAAATGGATCTAGGGTTTTTT
1 TGTGTGAAAATGGATCTAGGG-TTTTT
4277 TGTGTGAAAATGGATCTAGGGTTTTT
1 TGTGTGAAAATGGATCTAGGGTTTTT
4303 TGTGT
1 TGTGT
4308 TAAGATTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.45
Consensus pattern (26 bp):
TGTGTGAAAATGGATCTAGGGTTTTT
Found at i:12927 original size:29 final size:29
Alignment explanation
Indices: 12895--12964 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
12885 GCCGATGATA
* * **
12895 AAAAAAAAACATTTAAATATTTTATCATG
1 AAAAAAAAACATTAAAAAAAATTATCATG
*
12924 -AAAAAACACAATTAAAAAAAATTATCATG
1 AAAAAAAAAC-ATTAAAAAAAATTATCATG
12953 AAAAAACAAACA
1 AAAAAA-AAACA
12965 CACATAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 8 0.25
29 15 0.47
30 6 0.19
31 3 0.09
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (29 bp):
AAAAAAAAACATTAAAAAAAATTATCATG
Done.