Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012563.1 Kokia drynarioides strain JFW-HI SEQ_127572, 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: 11285
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1301 original size:30 final size:30
Alignment explanation
Indices: 1267--1342 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
1257 TTAAATTAGT
*
1267 AATGATAAAATTATACTTT-ATCCTTCCAAA
1 AATGATAAAATTATAATTTAATCCTT-CAAA
1297 AATGATAAAGATT-TAATTTAATCCTTCAAA
1 AATGATAAA-ATTATAATTTAATCCTTCAAA
* *
1327 AATTATAAAAATATAA
1 AATGATAAAATTATAA
1343 ACTATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 29 0.73
31 9 0.22
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (30 bp):
AATGATAAAATTATAATTTAATCCTTCAAA
Found at i:4562 original size:21 final size:20
Alignment explanation
Indices: 4535--4585 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
4525 TAAAACCCTA
*
4535 AATTTAAGGTTTAGGGTTTG
1 AATTTAAGGTTTAGGATTTG
*
4555 ATATTTAATGTTTAGGATTTG
1 A-ATTTAAGGTTTAGGATTTG
4576 AATTT-AGGTT
1 AATTTAAGGTT
4586 CAAGGTTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 18 0.67
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (20 bp):
AATTTAAGGTTTAGGATTTG
Found at i:6343 original size:13 final size:14
Alignment explanation
Indices: 6325--6353 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6315 CACGTGTTTT
6325 TTATTATTTAT-TA
1 TTATTATTTATATA
6338 TTATTATTTATATA
1 TTATTATTTATATA
6352 TT
1 TT
6354 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTTATATA
Found at i:6680 original size:4 final size:4
Alignment explanation
Indices: 6671--6736 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
6661 AAATAAACGG
* * * * *
6671 GAAA GAAA GAAA GAAAA GAAA GACA TACA GGAA GAAA GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
6721 G-AA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
6737 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.67, C:0.03, G:0.29, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:6821 original size:19 final size:19
Alignment explanation
Indices: 6776--6821 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
6766 GTATGATATC
*
6776 TTTTTAAAATCATATTTTA
1 TTTTTAAAATCATATTTAA
**
6795 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCATATTTAA
6815 TTTTTAA
1 TTTTTAA
6822 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCATATTTAA
Found at i:10050 original size:28 final size:28
Alignment explanation
Indices: 10011--10082 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
10001 CCCTCCTTAA
10011 TCAA-TCTAGTGTTTACGGTTT-AGAGTT
1 TCAAGTCTAGTGTTTACGGTTTAAG-GTT
10038 TCAAGTCTAGTGTTTACGGTTTAAGGTT
1 TCAAGTCTAGTGTTTACGGTTTAAGGTT
*
10066 TCAAGTCTAGAGTTTAC
1 TCAAGTCTAGTGTTTAC
10083 AATTTAGGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 4 0.10
28 36 0.86
29 2 0.05
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (28 bp):
TCAAGTCTAGTGTTTACGGTTTAAGGTT
Found at i:10088 original size:28 final size:27
Alignment explanation
Indices: 10011--10093 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
10001 CCCTCCTTAA
* **
10011 TCAA-TCTAGTGTTTACGGTTTAGAGTT
1 TCAAGTCTAGAGTTTACAATTTAG-GTT
* **
10038 TCAAGTCTAGTGTTTACGGTTTAAGGTT
1 TCAAGTCTAGAGTTTACAATTT-AGGTT
10066 TCAAGTCTAGAGTTTACAATTTAGGTT
1 TCAAGTCTAGAGTTTACAATTTAGGTT
10093 T
1 T
10094 TAGGTTTTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
27 10 0.20
28 39 0.76
29 2 0.04
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (27 bp):
TCAAGTCTAGAGTTTACAATTTAGGTT
Found at i:10346 original size:21 final size:21
Alignment explanation
Indices: 10320--10363 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10310 ATTAGGGTCC
* *
10320 ATTGCCCTAGAGGAGTAGAGT
1 ATTGCCCGAGAGGAATAGAGT
10341 ATTGCCCGAGAGGAATAGAGT
1 ATTGCCCGAGAGGAATAGAGT
10362 AT
1 AT
10364 CGCGGTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.23
Consensus pattern (21 bp):
ATTGCCCGAGAGGAATAGAGT
Found at i:10422 original size:45 final size:45
Alignment explanation
Indices: 10366--10494 Score: 213
Period size: 45 Copynumber: 2.9 Consensus size: 45
10356 TAGAGTATCG
*
10366 CGGTGACTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTA
1 CGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTA
*
10411 CGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTG
1 CGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTA
** *
10456 CGGTGGCTTATCAAACTGAGGCTGATATCCTTGGCTTGA
1 CGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGA
10495 TGAGCTATGC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.33
Consensus pattern (45 bp):
CGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTTGAGTATTA
Done.