Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009483.1 Kokia drynarioides strain JFW-HI SEQ_124192, 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: 26891
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:7762 original size:96 final size:96
Alignment explanation
Indices: 7581--7765 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
7571 AAAAAAGATG
** *
7581 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
* * *
7646 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAGAAAACATTACCTCGATTAAGGGTA
* *
7677 TTCGATTATTTTGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
*
7741 -AAAATAA-AATAATATTACCTCGATT
64 GAAAATAAGAA-AACATTACCTCGATT
7766 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 73 0.95
97 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
AAATAAGAAAACATTACCTCGATTAAGGGTA
Found at i:8149 original size:29 final size:28
Alignment explanation
Indices: 8099--8170 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
8089 GCAAAATGGT
*
8099 AATTTTTGAAAGTTTCGAGGTTAAAAATAG
1 AATTTTTGGAAG-TTCGAGGTTAAAAAT-G
*
8129 AATTTTTGGAAGTTCGGGGTTAAAAATG
1 AATTTTTGGAAGTTCGAGGTTAAAAATG
*
8157 AAATTTTGGAAGTT
1 AATTTTTGGAAGTT
8171 TTAGGGTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 14 0.36
29 14 0.36
30 11 0.28
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (28 bp):
AATTTTTGGAAGTTCGAGGTTAAAAATG
Found at i:8162 original size:89 final size:89
Alignment explanation
Indices: 7997--8163 Score: 212
Period size: 89 Copynumber: 1.9 Consensus size: 89
7987 TGGATACCCG
* * * *
7997 GGGGCAAAATGGTAATTTTGGGAAAATTTTGGGGTTAAAAATGGAATTTTAGGCATTCGAGGGTA
1 GGGGCAAAATGGTAATTTTGGGAAAATTTCGAGGTTAAAAATAGAATTTTAGGAATTCGAGGGTA
* *
8062 AAACGGTAATTTTTGGACATCCAT
66 AAAAGGAAATTTTTGGACATCCAT
* * *
8086 GGGGCAAAATGGTAATTTT-TGAAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTCG-GGGT
1 GGGGCAAAATGGTAATTTTGGGAAAATTTCGAGGTTAAAAATAGAATTTTAGGAA-TTCGAGGG-
*
8149 TAAAAATGAAATTTT
64 TAAAAAGGAAATTTT
8164 GGAAGTTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
88 31 0.47
89 35 0.53
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (89 bp):
GGGGCAAAATGGTAATTTTGGGAAAATTTCGAGGTTAAAAATAGAATTTTAGGAATTCGAGGGTA
AAAAGGAAATTTTTGGACATCCAT
Found at i:8177 original size:29 final size:29
Alignment explanation
Indices: 8102--8243 Score: 90
Period size: 29 Copynumber: 4.8 Consensus size: 29
8092 AAATGGTAAT
* * *
8102 TTTTGAAAGTTTCGAGGTTAAAAATAGAAT
1 TTTTGGAAGTTTAG-GGTTAAAAATAGAAA
**
8132 TTTTGGAAGTTCGGGGTTAAAAAT-GAAA
1 TTTTGGAAGTTTAGGGTTAAAAATAGAAA
* * * **
8160 TTTTGGAAGTTTTAGGGTCATAAATGGATTTT
1 TTTTGGAAG-TTTAGGGTTAAAAATAGA--AA
* *
8192 TTTTGGAAGTTTAGGGGTAAAAAT-GTAA
1 TTTTGGAAGTTTAGGGTTAAAAATAGAAA
* *
8220 TTTTCAGAAGTTTTGGGGTTAAAA
1 TTTT-GGAAG-TTTAGGGTTAAAA
8244 TGGATTTTTT
Statistics
Matches: 87, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
28 16 0.18
29 25 0.29
30 25 0.29
31 12 0.14
32 9 0.10
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGTTAAAAATAGAAA
Found at i:8195 original size:60 final size:60
Alignment explanation
Indices: 8131--8253 Score: 169
Period size: 60 Copynumber: 2.0 Consensus size: 60
8121 AAAAATAGAA
* *
8131 TTTTTGGAAG-TTCGGGGTTAAAAATGAAATTTT-GGAAGTTTTAGGGTCATAAATGGATTT
1 TTTTTGGAAGTTTAGGGG-TAAAAATGAAATTTTCAGAAGTTTTAGGGTCA-AAATGGATTT
* * *
8191 TTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTCAGAAGTTTTGGGGTTAAAATGGATTT
1 TTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTCAGAAGTTTTAGGGTCAAAATGGATTT
8251 TTT
1 TTT
8254 AAAAGTTTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 37 0.66
61 19 0.34
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.42
Consensus pattern (60 bp):
TTTTTGGAAGTTTAGGGGTAAAAATGAAATTTTCAGAAGTTTTAGGGTCAAAATGGATTT
Found at i:8223 original size:32 final size:32
Alignment explanation
Indices: 8160--8223 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
8150 AAAAATGAAA
* *
8160 TTTTGGAAGTTTTAGGGTCATAAATGGATTTT
1 TTTTGGAAGTTTTAGGGTCAAAAATGAATTTT
8192 TTTTGGAAG-TTTAGGGGT-AAAAATGTAATTTT
1 TTTTGGAAGTTTTA-GGGTCAAAAATG-AATTTT
8224 CAGAAGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.28, C:0.02, G:0.25, T:0.45
Consensus pattern (32 bp):
TTTTGGAAGTTTTAGGGTCAAAAATGAATTTT
Found at i:8244 original size:29 final size:29
Alignment explanation
Indices: 8197--8281 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
8187 ATTTTTTTTG
*
8197 GAAGTTTAGGGGTAAAAATGTAATTTTCA
1 GAAGTTTTGGGGTAAAAATGTAATTTTCA
* * * *
8226 GAAGTTTTGGGGTTAAAATGGATTTTTTA
1 GAAGTTTTGGGGTAAAAATGTAATTTTCA
* *
8255 AAAG-TTTGAGGGTAAAAATGTACTTTT
1 GAAGTTTTG-GGGTAAAAATGTAATTTT
8282 TTGGACAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
28 4 0.09
29 42 0.91
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (29 bp):
GAAGTTTTGGGGTAAAAATGTAATTTTCA
Found at i:8282 original size:29 final size:29
Alignment explanation
Indices: 8091--8282 Score: 88
Period size: 29 Copynumber: 6.5 Consensus size: 29
8081 TCCATGGGGC
* *
8091 AAAATGGTAATTTTTGAAAGTTTCGAGGTTA
1 AAAAT-GTAATTTTTAAAAGTTT-GAGGGTA
** *
8122 AAAATAG-AATTTTTGGAAGTTCG-GGGTTA
1 AAAAT-GTAATTTTTAAAAGTTTGAGGG-TA
* ** *
8151 AAAATG-AAATTTTGGAAGTTTTAGGGTCA
1 AAAATGTAATTTTTAAAAGTTTGAGGGT-A
* ** **
8180 TAAATGGATTTTTTTTGGAAGTTT-AGGGGTA
1 AAAAT-G-TAATTTTTAAAAGTTTGA-GGGTA
* * *
8211 AAAATGTAATTTTCAGAAGTTTTG-GGGTT
1 AAAATGTAATTTTTAAAAG-TTTGAGGGTA
* *
8240 AAAATGGATTTTTTAAAAGTTTGAGGGTA
1 AAAATGTAATTTTTAAAAGTTTGAGGGTA
*
8269 AAAATGTACTTTTT
1 AAAATGTAATTTTT
8283 TGGACAATTT
Statistics
Matches: 127, Mismatches: 24, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
28 21 0.17
29 60 0.47
30 18 0.14
31 12 0.09
32 16 0.13
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTTAAAAGTTTGAGGGTA
Found at i:10091 original size:17 final size:16
Alignment explanation
Indices: 10070--10159 Score: 81
Period size: 17 Copynumber: 5.1 Consensus size: 16
10060 AATACTAAGT
*
10070 TTTAAATCAATTTAAA
1 TTTAAATAAATTTAAA
*
10086 TTTTAATTAAATTTAAA
1 -TTTAAATAAATTTAAA
10103 TTTAAAAAAGATAAATTTAAA
1 TTT----AA-ATAAATTTAAA
10124 TTTAAGATAAATTTAAA
1 TTTAA-ATAAATTTAAA
10141 TTTAAAAATAAATTTAAA
1 TTT--AAATAAATTTAAA
10159 T
1 T
10160 CAATTTAAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.05
17 31 0.49
18 12 0.19
19 2 0.03
20 2 0.03
21 13 0.21
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATAAATTTAAA
Found at i:10093 original size:6 final size:6
Alignment explanation
Indices: 10078--10159 Score: 68
Period size: 6 Copynumber: 14.5 Consensus size: 6
10068 GTTTTAAATC
* **
10078 AATTTA AATTTT AA-TTA AATTTA AATTTA AA---A AAGATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
**
10122 AATTTA AGA--TA AATTTA AATTTA AAAATA AATTTA AAT
1 AATTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA AAT
10160 CAATTTAAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 3 0.05
4 1 0.02
5 7 0.11
6 49 0.80
7 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:10121 original size:38 final size:36
Alignment explanation
Indices: 10073--10159 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 36
10063 ACTAAGTTTT
* *
10073 AAATCAATTTAAATTTTAA-TTAAATTTAAATTTAAAA
1 AAATAAATTTAAATTTTAAGATAAATTTAAATTT--AA
10110 AAGATAAATTTAAA-TTTAAGATAAATTTAAATTTAA
1 AA-ATAAATTTAAATTTTAAGATAAATTTAAATTTAA
10146 AAATAAATTTAAAT
1 AAATAAATTTAAAT
10160 CAATTTAAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 11 0.24
36 4 0.09
37 7 0.16
38 23 0.51
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (36 bp):
AAATAAATTTAAATTTTAAGATAAATTTAAATTTAA
Found at i:10404 original size:2 final size:2
Alignment explanation
Indices: 10397--10435 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10387 TTAAACACAT
10397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10436 TTAAAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16047 original size:22 final size:21
Alignment explanation
Indices: 16010--16062 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
16000 TTTCAATAAA
*
16010 AGAGAAAAATATGGATTTTAT
1 AGAGAAAAATATGGATTTTAC
16031 AGAGAAAAACT-TGGGATTTTAC
1 AGAGAAAAA-TAT-GGATTTTAC
*
16053 AAAGAAAAAT
1 AGAGAAAAAT
16063 CATTTTACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (21 bp):
AGAGAAAAATATGGATTTTAC
Found at i:16600 original size:12 final size:12
Alignment explanation
Indices: 16572--16603 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16562 TTTACCAAAG
16572 TAATTTT-TAAA
1 TAATTTTATAAA
16583 -AATTTTATAAA
1 TAATTTTATAAA
16594 TAATTTTATA
1 TAATTTTATA
16604 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.32
11 4 0.21
12 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATTTTATAAA
Found at i:17508 original size:21 final size:22
Alignment explanation
Indices: 17469--17517 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
17459 GTTATTTTAG
** *
17469 TTTTTTATTTATTTTATTTATC
1 TTTTTTATTTATTGGATTTATA
*
17491 TTTTTTA-TTATTGGATTTGTA
1 TTTTTTATTTATTGGATTTATA
17512 TTTTTT
1 TTTTTT
17518 TTTTGTCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTTTTATTTATTGGATTTATA
Found at i:17704 original size:27 final size:27
Alignment explanation
Indices: 17628--17728 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
17618 TAAAAATTCA
*
17628 AAAAATTTATAAAAACTATTCTTAAAA-AT
1 AAAAA-TTAT-AAAA-TATTTTTAAAATAT
* ** *
17657 AAAAATCATTTAATTTATTTTAAAATAT
1 AAAAATTATAAAATAT-TTTTAAAATAT
* *
17685 AAAAATTATAAAATATTTTTAAATTTT
1 AAAAATTATAAAATATTTTTAAAATAT
* *
17712 AAAAATAATTAAATATT
1 AAAAATTATAAAATATT
17729 GACATGTCAT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
26 2 0.04
27 33 0.58
28 17 0.30
29 5 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAATTATAAAATATTTTTAAAATAT
Found at i:23113 original size:19 final size:18
Alignment explanation
Indices: 23091--23145 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
23081 ATTATAAAAT
*
23091 AATTTAAAATAATTTTTAA
1 AATTTAAAAT-ATTTATAA
*
23110 AATTTTAAATATTTATAAA
1 AATTTAAAATATTTAT-AA
23129 AATTCTAAAA-ATTTATA
1 AATT-TAAAATATTTATA
23146 TTTTAATACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.19
19 21 0.68
20 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTAAAATATTTATAA
Done.