Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000498.1 Kokia drynarioides strain JFW-HI SEQ_111374, 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: 35468
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:3461 original size:80 final size:80
Alignment explanation
Indices: 3327--3477 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 80
3317 CAAATTCGTT
** * * * * *
3327 AATTCATGACACCTGATGCCTAGTGGATAAACCGCGATAAGTGAGCCCAGCTCTAATTGGATTAA
1 AATTCATGACACCCAATGCCTAGCGGATAAACCACAATAAATGAGCCCAACTCTAATTGGATTAA
3392 CCAACGAATTCCATC
66 CCAACGAATTCCATC
* * * *
3407 AATTCATGCCACCCAATGCCTGGCGGATAAACCATAATAAATGAGCCCAACTCTAGTTGGATTAA
1 AATTCATGACACCCAATGCCTAGCGGATAAACCACAATAAATGAGCCCAACTCTAATTGGATTAA
3472 CCAACG
66 CCAACG
3478 GTTTGCGCCC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (80 bp):
AATTCATGACACCCAATGCCTAGCGGATAAACCACAATAAATGAGCCCAACTCTAATTGGATTAA
CCAACGAATTCCATC
Found at i:7486 original size:22 final size:21
Alignment explanation
Indices: 7461--7502 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
7451 GATAATGAGA
7461 TACATGTCTTGAAATTAGATCT
1 TACATGTCTTGAAATT-GATCT
*
7483 TACATGTCTTGAGATTGATC
1 TACATGTCTTGAAATTGATC
7503 AAGAGACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (21 bp):
TACATGTCTTGAAATTGATCT
Found at i:9186 original size:9 final size:9
Alignment explanation
Indices: 9161--9194 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
9151 AATATGAATA
9161 ATTAATTATT
1 ATTAA-TATT
9171 AATTAATATT
1 -ATTAATATT
9181 ATTAATATT
1 ATTAATATT
9190 ATTAA
1 ATTAA
9195 AATGACTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 4 0.17
11 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTAATATT
Found at i:9723 original size:23 final size:23
Alignment explanation
Indices: 9696--9743 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
9686 AAAATTTAAT
* *
9696 TTTAATATTTTTATTTTTAAAAA
1 TTTAATATTTTTACTTTAAAAAA
*
9719 TTTAATCTTTTTACTTTAAAAAA
1 TTTAATATTTTTACTTTAAAAAA
9742 TT
1 TT
9744 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAATATTTTTACTTTAAAAAA
Found at i:9745 original size:22 final size:23
Alignment explanation
Indices: 9697--9745 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
9687 AAATTTAATT
* *
9697 TTAATATTTTTATTTTTAAAAAT
1 TTAATATTTTTATCTTTAAAAAA
*
9720 TTAATCTTTTTA-CTTTAAAAAA
1 TTAATATTTTTATCTTTAAAAAA
9742 TTAA
1 TTAA
9746 AAATTAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATATTTTTATCTTTAAAAAA
Found at i:19516 original size:2 final size:2
Alignment explanation
Indices: 19509--19535 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19499 GACAATAAGC
19509 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19536 CTATCATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22650 original size:7 final size:6
Alignment explanation
Indices: 22623--22648 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22613 AAAAATTTAG
22623 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
22649 TAATCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:24059 original size:16 final size:15
Alignment explanation
Indices: 24023--24069 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
24013 TTTGATTCTG
24023 TTTAATTTT-ATAAA
1 TTTAATTTTGATAAA
**
24037 TGAAATTTTGATCAAA
1 TTTAATTTTGAT-AAA
*
24053 TTTAATTCTGATAAA
1 TTTAATTTTGATAAA
24068 TT
1 TT
24070 AATAACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 7 0.27
15 7 0.27
16 12 0.46
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (15 bp):
TTTAATTTTGATAAA
Found at i:29569 original size:24 final size:24
Alignment explanation
Indices: 29531--29592 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
29521 GAGAATCAAT
* * *
29531 TTTTAAGTTAAACTCTATTTATTTG
1 TTTTAA-TCAAACTCAATTTATTCG
29556 TTTTAATCAAACTCAATTTATTCG
1 TTTTAATCAAACTCAATTTATTCG
* *
29580 TCTCAATCAAACT
1 TTTTAATCAAACT
29593 TTGATTAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (24 bp):
TTTTAATCAAACTCAATTTATTCG
Found at i:33986 original size:29 final size:30
Alignment explanation
Indices: 33948--34013 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
33938 ATTTAATGTG
* * * *
33948 TAATTGTATATAT-AAATTTTTATTTTATA
1 TAATTTTATACATAAAATTTTGATTTAATA
*
33977 TAATTTTATACATAAAATTTTGATTTAATC
1 TAATTTTATACATAAAATTTTGATTTAATA
34007 TAATTTT
1 TAATTTT
34014 GATAAATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (30 bp):
TAATTTTATACATAAAATTTTGATTTAATA
Done.