Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011951.1 Kokia drynarioides strain JFW-HI SEQ_126949, 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: 30947
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:882 original size:32 final size:32
Alignment explanation
Indices: 845--959 Score: 97
Period size: 32 Copynumber: 3.4 Consensus size: 32
835 TAATCACTTT
845 AATATTAAATTAATATAATACTTATCAAGAAA
1 AATATTAAATTAATATAATACTTATCAAGAAA
* * ****
877 AATATTAGAGTTCAACTATAATTAAATTTAATC-ACTTT
1 AATATTA-AATT-AA-TATAA-T--ACTT-ATCAAGAAA
915 AATATTAAATTAATATAATACTTATCAAGAAA
1 AATATTAAATTAATATAATACTTATCAAGAAA
*
947 AATATTAGATTAA
1 AATATTAAATTAA
960 ATTTAATATT
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
31 3 0.05
32 23 0.37
33 3 0.05
34 3 0.05
35 10 0.16
36 3 0.05
37 3 0.05
38 11 0.18
39 3 0.05
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.37
Consensus pattern (32 bp):
AATATTAAATTAATATAATACTTATCAAGAAA
Found at i:895 original size:70 final size:70
Alignment explanation
Indices: 813--955 Score: 286
Period size: 70 Copynumber: 2.0 Consensus size: 70
803 GAGAGTTTAG
813 AGAGTTCAACTATAATTAAATTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAA
1 AGAGTTCAACTATAATTAAATTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAA
878 ATATT
66 ATATT
883 AGAGTTCAACTATAATTAAATTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAA
1 AGAGTTCAACTATAATTAAATTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAA
948 ATATT
66 ATATT
953 AGA
1 AGA
956 TTAAATTTAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (70 bp):
AGAGTTCAACTATAATTAAATTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAA
ATATT
Found at i:932 original size:35 final size:35
Alignment explanation
Indices: 823--933 Score: 104
Period size: 35 Copynumber: 3.2 Consensus size: 35
813 AGAGTTCAAC
823 TATAATTAAATTTAATCACTTTAATATTAAATTAA
1 TATAATTAAATTTAATCACTTTAATATTAAATTAA
* **** *
858 TATAA-T--ACTT-ATCAAGAAAAATATTAGAGTTCAA
1 TATAATTAAATTTAATC-ACTTTAATATTA-AATT-AA
892 CTATAATTAAATTTAATCACTTTAATATTAAATTAA
1 -TATAATTAAATTTAATCACTTTAATATTAAATTAA
928 TATAAT
1 TATAAT
934 ACTTATCAAG
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
31 3 0.05
32 11 0.20
33 3 0.05
34 3 0.05
35 16 0.29
36 3 0.05
37 3 0.05
38 11 0.20
39 3 0.05
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (35 bp):
TATAATTAAATTTAATCACTTTAATATTAAATTAA
Found at i:971 original size:70 final size:68
Alignment explanation
Indices: 835--1092 Score: 245
Period size: 70 Copynumber: 3.9 Consensus size: 68
825 TAATTAAATT
* * *
835 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAAATATTAGAGTTCAA-CT-ATAA
1 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAAATATTA-AATTAAATTTAAT-A
898 TTAAA
64 TTAAA
*
903 TTTAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAAATATTAGATTAAATTTAATA
1 --TAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAAATATTAAATTAAATTTAATA
968 TT--A
64 TTAAA
* * * *
971 -AAT-A---T--TATTAAATTAATAGAATATTTATCTACAAAATAAACATTAAAATT-AATTTAA
1 TAATCACTTTAATATTAAATTAATATAATACTTATC-A-AGAA-AAATATT-AAATTAAATTTAA
1028 TATTAAA
62 TATTAAA
* ** *
1035 TAATCACTTTAATATTAAATTAATAAAATAC-TATCAAGATCATTATTAAATTAAATTT
1 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAAATATTAAATTAAATTT
1093 TTATAAATGT
Statistics
Matches: 156, Mismatches: 16, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
59 22 0.14
60 1 0.01
61 4 0.03
62 17 0.11
63 4 0.03
64 2 0.01
65 6 0.04
66 6 0.04
67 9 0.06
68 3 0.02
69 6 0.04
70 57 0.37
71 19 0.12
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATATAATACTTATCAAGAAAAATATTAAATTAAATTTAATATT
AAA
Found at i:988 original size:59 final size:62
Alignment explanation
Indices: 917--1036 Score: 158
Period size: 59 Copynumber: 2.0 Consensus size: 62
907 ATCACTTTAA
* * * *
917 TATTAAATTAATATAATACTTATC-A-AGAA-AAATATT-AGATTAAATTTAATATTAAATAT
1 TATTAAATTAATAGAATACTTATCTACAAAATAAACATTAAAATT-AATTTAATATTAAATAT
*
976 TATTAAATTAATAGAATATTTATCTACAAAATAAACATTAAAATTAATTTAATATTAAATA
1 TATTAAATTAATAGAATACTTATCTACAAAATAAACATTAAAATTAATTTAATATTAAATA
1037 ATCACTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 3 0.06
62 22 0.42
63 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (62 bp):
TATTAAATTAATAGAATACTTATCTACAAAATAAACATTAAAATTAATTTAATATTAAATAT
Found at i:1985 original size:21 final size:21
Alignment explanation
Indices: 1946--2000 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1936 AGGTAAGAAA
* **
1946 ATAAAAATATATAAAATTATT
1 ATAAAAATAAATAAAATTACC
* *
1967 ATAAAAATAAATTATATTACC
1 ATAAAAATAAATAAAATTACC
*
1988 ATAAATATAAATA
1 ATAAAAATAAATA
2001 TTATTTAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAAATAAATAAAATTACC
Found at i:3553 original size:5 final size:5
Alignment explanation
Indices: 3543--3575 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
3533 AATATTGCAT
3543 AAATA AAATA AAATA AAATA AAATGA AAATA AA
1 AAATA AAATA AAATA AAATA AAAT-A AAATA AA
3576 TATACTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:3576 original size:15 final size:14
Alignment explanation
Indices: 3541--3577 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
3531 AAAATATTGC
3541 ATAAATAAAATAAA
1 ATAAATAAAATAAA
3555 ATAAAATAAAATGAAA
1 AT-AAATAAAAT-AAA
3571 ATAAATA
1 ATAAATA
3578 TACTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 14 0.67
16 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
ATAAATAAAATAAA
Found at i:4704 original size:18 final size:18
Alignment explanation
Indices: 4681--4717 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4671 AGCTCCATAG
4681 TTGACAAGTCATATAACT
1 TTGACAAGTCATATAACT
4699 TTGACAAGTCATATAACT
1 TTGACAAGTCATATAACT
4717 T
1 T
4718 CCTCTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (18 bp):
TTGACAAGTCATATAACT
Found at i:6777 original size:25 final size:23
Alignment explanation
Indices: 6747--6792 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
6737 ATTGGATCCA
6747 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
6772 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
6793 CCCTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:10758 original size:31 final size:31
Alignment explanation
Indices: 10720--10779 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
10710 TACAATGTAT
* * *
10720 ACAGATTAAATTTTAAATTTAAACATATTAA
1 ACAGATTAAAATTGAAAATTAAACATATTAA
*
10751 ACAGATTAAAATTGAAAATTAACCATATT
1 ACAGATTAAAATTGAAAATTAAACATATT
10780 TATAAAATGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (31 bp):
ACAGATTAAAATTGAAAATTAAACATATTAA
Found at i:20446 original size:84 final size:84
Alignment explanation
Indices: 20305--20485 Score: 326
Period size: 84 Copynumber: 2.2 Consensus size: 84
20295 TAAAAGAATA
*
20305 TTATGCAAAAGAACACATATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
1 TTATGCAAAAGAACACACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
*
20370 GAAACACCAAATCGACAAT
66 AAAACACCAAATCGACAAT
*
20389 TTATGCAAAAGAACATACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
1 TTATGCAAAAGAACACACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
20454 AAAACACCAAATCGACAAT
66 AAAACACCAAATCGACAAT
*
20473 TTATGTAAAAGAA
1 TTATGCAAAAGAA
20486 TATTATGTAA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 93 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.23
Consensus pattern (84 bp):
TTATGCAAAAGAACACACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
AAAACACCAAATCGACAAT
Found at i:20560 original size:99 final size:99
Alignment explanation
Indices: 20389--20574 Score: 354
Period size: 99 Copynumber: 1.9 Consensus size: 99
20379 AATCGACAAT
20389 TTATGCAAAAGAACATACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
1 TTATGCAAAAGAACATACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
20454 AAAACACCAAATCGACAATTTATGTAAAAGAATA
66 AAAACACCAAATCGACAATTTATGTAAAAGAATA
* *
20488 TTATGTAAAAGAACATATATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
1 TTATGCAAAAGAACATACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
20553 AAAACACCAAATCGACAATTTA
66 AAAACACCAAATCGACAATTTA
20575 CTACTTAAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 85 1.00
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.25
Consensus pattern (99 bp):
TTATGCAAAAGAACATACATACCATAACAACCCATGTGTCATACATCAAGCTAACATTTATATCC
AAAACACCAAATCGACAATTTATGTAAAAGAATA
Found at i:22797 original size:13 final size:13
Alignment explanation
Indices: 22775--22806 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
22765 TACAAACAAA
*
22775 ACTATAAATTAAC
1 ACTATTAATTAAC
22788 ACTATTAATTAAC
1 ACTATTAATTAAC
22801 ACTATT
1 ACTATT
22807 CCTAGCCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (13 bp):
ACTATTAATTAAC
Found at i:23137 original size:7 final size:7
Alignment explanation
Indices: 23103--23207 Score: 50
Period size: 7 Copynumber: 15.0 Consensus size: 7
23093 AACCCAAAAA
23103 GTCAACG
1 GTCAACG
* *
23110 ATCAACA
1 GTCAACG
* *
23117 GTTAACA
1 GTCAACG
*
23124 GTAAACG
1 GTCAACG
23131 GTCAACG
1 GTCAACG
*
23138 ATCAACG
1 GTCAACG
*
23145 GTCAATG
1 GTCAACG
* **
23152 ATCAAAT
1 GTCAACG
*
23159 GTTAACG
1 GTCAACG
*
23166 ATCAAAC-
1 GTC-AACG
* **
23173 ATCAATA
1 GTCAACG
23180 GTCAACG
1 GTCAACG
*
23187 ATCAACG
1 GTCAACG
23194 GTCAACG
1 GTCAACG
23201 GTCAACG
1 GTCAACG
23208 AGTCGGGTTG
Statistics
Matches: 71, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
6 2 0.03
7 66 0.93
8 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:23146 original size:14 final size:14
Alignment explanation
Indices: 23103--23208 Score: 65
Period size: 14 Copynumber: 7.6 Consensus size: 14
23093 AACCCAAAAA
*
23103 GTCAACGATCAACA
1 GTCAACGATCAACG
* *
23117 GTTAAC-AGTAAACG
1 GTCAACGA-TCAACG
23131 GTCAACGATCAACG
1 GTCAACGATCAACG
* **
23145 GTCAATGATCAAAT
1 GTCAACGATCAACG
*
23159 GTTAACGATCAAAC-
1 GTCAACGATC-AACG
* *
23173 ATCAA-TAGTCAACG
1 GTCAACGA-TCAACG
* *
23187 ATCAACGGTCAACG
1 GTCAACGATCAACG
23201 GTCAACGA
1 GTCAACGA
23209 GTCGGGTTGG
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
13 5 0.07
14 60 0.88
15 3 0.04
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (14 bp):
GTCAACGATCAACG
Found at i:23305 original size:24 final size:24
Alignment explanation
Indices: 23272--23328 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
23262 GGGTTCACTT
*
23272 GGTTTAGGTCAAAAAGTTTATAAG
1 GGTTTGGGTCAAAAAGTTTATAAG
*
23296 GGTTTGGGTCAAAAGGTTTATAAG
1 GGTTTGGGTCAAAAAGTTTATAAG
23320 GGTTTGGGT
1 GGTTTGGGT
23329 TTATAAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (24 bp):
GGTTTGGGTCAAAAAGTTTATAAG
Done.