Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008970.1 Kokia drynarioides strain JFW-HI SEQ_123667, 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: 54888
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:913 original size:5 final size:5
Alignment explanation
Indices: 874--914 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
864 CCATTCAGGG
* * *
874 AAGGG AAGGG AAGGT AAGGG AAGGT AAGGT AAGGT AAGGT A
1 AAGGT AAGGT AAGGT AAGGT AAGGT AAGGT AAGGT AAGGT A
915 CAGAACGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.12
Consensus pattern (5 bp):
AAGGT
Found at i:913 original size:15 final size:15
Alignment explanation
Indices: 874--914 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
864 CCATTCAGGG
*
874 AAGGGAAGGGAAGGT
1 AAGGGAAGGTAAGGT
889 AAGGGAAGGTAAGGT
1 AAGGGAAGGTAAGGT
*
904 AAGGTAAGGTA
1 AAGGGAAGGTA
915 CAGAACGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.12
Consensus pattern (15 bp):
AAGGGAAGGTAAGGT
Found at i:914 original size:10 final size:10
Alignment explanation
Indices: 870--912 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
860 AGAACCATTC
*
870 AGGGAAGGGA
1 AGGGAAGGTA
880 AGGGAAGGTA
1 AGGGAAGGTA
890 AGGGAAGGTA
1 AGGGAAGGTA
*
900 AGGTAAGGTA
1 AGGGAAGGTA
910 AGG
1 AGG
913 TACAGAACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (10 bp):
AGGGAAGGTA
Found at i:1184 original size:92 final size:92
Alignment explanation
Indices: 1027--1234 Score: 407
Period size: 92 Copynumber: 2.3 Consensus size: 92
1017 GGTGGGAATA
*
1027 AAACACATACCTTATTTGAAGCTTCTACTTATTTGTTAAAGGTGATGAGAAGTTTAGCTTGAATT
1 AAACACATACCTTATTTGAAGCTTCTACTTATGTGTTAAAGGTGATGAGAAGTTTAGCTTGAATT
1092 ATTGCATGAATAATAAATAAGCAGAGG
66 ATTGCATGAATAATAAATAAGCAGAGG
1119 AAACACATACCTTATTTGAAGCTTCTACTTATGTGTTAAAGGTGATGAGAAGTTTAGCTTGAATT
1 AAACACATACCTTATTTGAAGCTTCTACTTATGTGTTAAAGGTGATGAGAAGTTTAGCTTGAATT
1184 ATTGCATGAATAATAAATAAGCAGAGG
66 ATTGCATGAATAATAAATAAGCAGAGG
1211 AAACACATACCTTATTTGAAGCTT
1 AAACACATACCTTATTTGAAGCTT
1235 TATTTTGGAC
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 115 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (92 bp):
AAACACATACCTTATTTGAAGCTTCTACTTATGTGTTAAAGGTGATGAGAAGTTTAGCTTGAATT
ATTGCATGAATAATAAATAAGCAGAGG
Found at i:3629 original size:2 final size:2
Alignment explanation
Indices: 3622--3651 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3612 TAAAGGGATA
3622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3652 TCTCTTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3918 original size:17 final size:17
Alignment explanation
Indices: 3889--3921 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3879 CAATAATTAA
3889 ATAAATAATTAAAAAAT
1 ATAAATAATTAAAAAAT
3906 ATAAA-AATATAAAAAA
1 ATAAATAAT-TAAAAAA
3922 CGTAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAATAATTAAAAAAT
Found at i:10722 original size:23 final size:24
Alignment explanation
Indices: 10677--10722 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
10667 CTTTTCTTTA
*
10677 GGTTTATATTTTTTTTATCAATTT
1 GGTTTATATTTTTTTTATAAATTT
10701 GGTTT-TATTTTATTTT-TAAATT
1 GGTTTATATTTT-TTTTATAAATT
10723 GATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (24 bp):
GGTTTATATTTTTTTTATAAATTT
Found at i:15293 original size:6 final size:6
Alignment explanation
Indices: 15282--15311 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
15272 TGAGTAACAT
*
15282 AGGCAA AGGCAA AGGCAA AGGCAA TGGCAA
1 AGGCAA AGGCAA AGGCAA AGGCAA AGGCAA
15312 GAAAGAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.33, T:0.03
Consensus pattern (6 bp):
AGGCAA
Found at i:17197 original size:4 final size:4
Alignment explanation
Indices: 17188--17219 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
17178 GGGCATGGGG
17188 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TCCC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TCCC
17220 ACCACTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (4 bp):
TCCC
Found at i:19783 original size:2 final size:2
Alignment explanation
Indices: 19778--19806 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19768 AGAGAGAGAG
19778 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19807 TTGGAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25201 original size:23 final size:21
Alignment explanation
Indices: 25121--25202 Score: 56
Period size: 23 Copynumber: 3.5 Consensus size: 21
25111 AAGTGTTGGG
*
25121 TAACAGAGGGCACACAAACTGC
1 TAACAGAGGGCACAC-AAGTGC
* *
25143 TAATCAGAGAGCACACGAAGCGC
1 TAA-CAGAGGGCACAC-AAGTGC
*
25166 TAATAACAAAGGGCACACACAGTGC
1 ---TAACAGAGGGCACACA-AGTGC
25191 TGAACAGAGGGC
1 T-AACAGAGGGC
25203 GCGCTAGTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
22 4 0.09
23 24 0.52
24 1 0.02
25 14 0.30
26 3 0.07
ACGTcount: A:0.40, C:0.24, G:0.26, T:0.10
Consensus pattern (21 bp):
TAACAGAGGGCACACAAGTGC
Found at i:36286 original size:16 final size:18
Alignment explanation
Indices: 36265--36298 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
36255 CACTAACCCA
36265 TTTTTTA-ATTTT-TTTT
1 TTTTTTACATTTTGTTTT
36281 TTTTTTACATTTTGTTTT
1 TTTTTTACATTTTGTTTT
36299 AATTCAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTTACATTTTGTTTT
Found at i:48560 original size:41 final size:41
Alignment explanation
Indices: 48514--48609 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
48504 GAATTTTATT
*
48514 TTAACAAGAATTCTAGTCACCCAATTTTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
48555 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
48596 TTGACAAGAATTCT
1 TTAACAAGAATTCT
48610 CTACGAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Done.