Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011721.1 Kokia drynarioides strain JFW-HI SEQ_126715, 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: 79331
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:8691 original size:58 final size:57
Alignment explanation
Indices: 8551--8842 Score: 236
Period size: 59 Copynumber: 5.0 Consensus size: 57
8541 TTTTGGGAAA
* * * *
8551 TTTTGGGGTTAAAAATGAAATTTTAGATATTCAGGGGT-AAAATGGTAA-TTTTAGAAA-
1 TTTTGGGGTCAAAAATGGAATTTTGGA-ATTCGGGGGTAAAAAT-GTAATTTTTA-AAAG
** * * * *
8608 AATCGGGATAAAAAAT-GACATTTTTGGACATTCGGGGGT-AAAATGGTAAATTTTAAAAG
1 TTTTGGGGTCAAAAATGGA-A-TTTTGGA-ATTCGGGGGTAAAAAT-GTAATTTTTAAAAG
** * *
8667 TTTTGGGGTCAAAAATGGAATTTTGGAAATTTTGGGGTAAAAATGTAACTTTTGAAAG
1 TTTTGGGGTCAAAAATGGAATTTTGG-AATTCGGGGGTAAAAATGTAATTTTTAAAAG
* * * * * *
8725 TTTTAGGGTCAAAAATAGATTTTTTGGAAGTTCGAGGGTAAAAATTTAATTTTTGAAAG
1 TTTTGGGGTCAAAAATGGA-ATTTTGGAA-TTCGGGGGTAAAAATGTAATTTTTAAAAG
*
8784 TTTTGGGGTTAAAAATGGAATTTTTGGAAGTT-GGAGGGTAAAAATGTAATTTTTAAAAG
1 TTTTGGGGTCAAAAATGGAA-TTTTGGAA-TTCGG-GGGTAAAAATGTAATTTTTAAAAG
8843 CTTCGAGGTC
Statistics
Matches: 191, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.01
57 12 0.06
58 74 0.39
59 102 0.53
60 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (57 bp):
TTTTGGGGTCAAAAATGGAATTTTGGAATTCGGGGGTAAAAATGTAATTTTTAAAAG
Found at i:8750 original size:30 final size:29
Alignment explanation
Indices: 8643--8842 Score: 170
Period size: 29 Copynumber: 6.8 Consensus size: 29
8633 GGACATTCGG
* * *
8643 GGGT-AAAATGGTAAATTTTAAAAGTTTTG
1 GGGTAAAAATGG-AATTTTTGAAAGTTTTA
* *
8672 GGGTCAAAAATGGAATTTTGGAAA-TTTTG
1 GGGT-AAAAATGGAATTTTTGAAAGTTTTA
* *
8701 GGGTAAAAATGTAACTTTTGAAAGTTTTA
1 GGGTAAAAATGGAATTTTTGAAAGTTTTA
* * * **
8730 GGGTCAAAAATAGATTTTTTGGAAGTTCGA
1 GGGT-AAAAATGGAATTTTTGAAAGTTTTA
** *
8760 GGGTAAAAATTTAATTTTTGAAAGTTTTG
1 GGGTAAAAATGGAATTTTTGAAAGTTTTA
* **
8789 GGGTTAAAAATGGAATTTTTGGAAGTTGGA
1 GGG-TAAAAATGGAATTTTTGAAAGTTTTA
* *
8819 GGGTAAAAATGTAATTTTTAAAAG
1 GGGTAAAAATGGAATTTTTGAAAG
8843 CTTCGAGGTC
Statistics
Matches: 136, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
28 16 0.12
29 60 0.44
30 53 0.39
31 7 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGAAAGTTTTA
Found at i:10042 original size:28 final size:24
Alignment explanation
Indices: 10005--10063 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 24
9995 AGAATATTAT
*
10005 TATTATTATTAATGTTGTAATTAATAA
1 TATTAATATT-ATGTT-TAA-TAATAA
*
10032 TAATTAATATTATGTTTAATATTAA
1 T-ATTAATATTATGTTTAATAATAA
10057 TATTAAT
1 TATTAAT
10064 GATAATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 6 0.21
25 6 0.21
26 3 0.10
27 6 0.21
28 8 0.28
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (24 bp):
TATTAATATTATGTTTAATAATAA
Found at i:10844 original size:6 final size:6
Alignment explanation
Indices: 10833--10883 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
10823 TCAAATTTGA
* *
10833 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT TTAGGA- -TAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT
10879 TTAAA
1 TTAAA
10884 AAAAAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 1 0.03
5 6 0.16
6 29 0.78
7 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:10856 original size:17 final size:18
Alignment explanation
Indices: 10834--10895 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 18
10824 CAAATTTGAT
10834 TAAATTTAAATTTAAAG-
1 TAAATTTAAATTTAAAGA
*
10851 TAAATTTAAATTT-AGGA
1 TAAATTTAAATTTAAAGA
*
10868 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAGA
*
10886 AAAATTTAAA
1 TAAATTTAAA
10896 CCAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
16 2 0.05
17 26 0.67
18 11 0.28
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (18 bp):
TAAATTTAAATTTAAAGA
Found at i:11228 original size:14 final size:14
Alignment explanation
Indices: 11209--11238 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11199 TGTTTGGCGC
11209 AAATGAGGATAGAG
1 AAATGAGGATAGAG
11223 AAATGAGGATAGAG
1 AAATGAGGATAGAG
11237 AA
1 AA
11239 CTGTAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.13
Consensus pattern (14 bp):
AAATGAGGATAGAG
Found at i:18447 original size:37 final size:37
Alignment explanation
Indices: 18397--18471 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
18387 CTTGCACACA
*
18397 TGTATTTGAATTTGAGTCAGATTTCGGATTTTCGAAT
1 TGTATTTGAATTTGAGTCAGACTTCGGATTTTCGAAT
18434 TGTATTTGAATTTGAGTCAGACTTCGGATTTTCGAAT
1 TGTATTTGAATTTGAGTCAGACTTCGGATTTTCGAAT
18471 T
1 T
18472 TGGATATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (37 bp):
TGTATTTGAATTTGAGTCAGACTTCGGATTTTCGAAT
Found at i:19152 original size:53 final size:53
Alignment explanation
Indices: 19081--19186 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
19071 AAATATAAAA
19081 TGCATGAGATTTGCTCTATCAATATTATTAGCCCTGTTTGCTCTTATATTTGT
1 TGCATGAGATTTGCTCTATCAATATTATTAGCCCTGTTTGCTCTTATATTTGT
* *
19134 TGCATGAGATTTGTTCTATCAATATTATTCGCCCTGTTTGCTCTTATATTTGT
1 TGCATGAGATTTGCTCTATCAATATTATTAGCCCTGTTTGCTCTTATATTTGT
19187 CGTTCTTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (53 bp):
TGCATGAGATTTGCTCTATCAATATTATTAGCCCTGTTTGCTCTTATATTTGT
Found at i:22139 original size:19 final size:19
Alignment explanation
Indices: 22097--22141 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
22087 TCATTTGTCA
* *
22097 ATATGCACTTCGTGTCCCG
1 ATATGCACTTCATGTCCAG
22116 ATATGCACTTCATGTGCCAG
1 ATATGCACTTCATGT-CCAG
22136 -TATGCA
1 ATATGCA
22142 TTACGATGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (19 bp):
ATATGCACTTCATGTCCAG
Found at i:22448 original size:17 final size:17
Alignment explanation
Indices: 22426--22458 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
22416 TGTGACATGT
22426 GACTATTAGAGTTGTGC
1 GACTATTAGAGTTGTGC
22443 GACTATTAGAGTTGTG
1 GACTATTAGAGTTGTG
22459 TGACCCGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.30, T:0.36
Consensus pattern (17 bp):
GACTATTAGAGTTGTGC
Found at i:26374 original size:51 final size:53
Alignment explanation
Indices: 26273--26374 Score: 138
Period size: 51 Copynumber: 1.9 Consensus size: 53
26263 ATTTCTTAAG
*
26273 AATATTGCTTCTTTTGGATAAATTAGTTTTATGTTTAAATCGATTTTCATGTTCA
1 AATATTGCTTCTTTTGG--AAATTAGTTTTATGTTTAAATCGATTGTCATGTTCA
*
26328 AATATTGCTTCTTTT-G-AATT-GTTTATATGTTTAGATCGATTGTCATG
1 AATATTGCTTCTTTTGGAAATTAGTTT-TATGTTTAAATCGATTGTCATG
26375 CTGGAATACT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
50 4 0.09
51 24 0.55
54 1 0.02
55 15 0.34
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (53 bp):
AATATTGCTTCTTTTGGAAATTAGTTTTATGTTTAAATCGATTGTCATGTTCA
Found at i:26391 original size:51 final size:51
Alignment explanation
Indices: 26293--26393 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
26283 CTTTTGGATA
* * *
26293 AATTAGTTTTATGTTTAAATCGATTTTCATGTTCAAATATTGCTTCTTTTG
1 AATTAGTTTTATGTTTAAATCGATTGTCATGCTCAAATACTGCTTCTTTTG
* ** *
26344 AATT-GTTTATATGTTTAGATCGATTGTCATGCTGGAATACTGTTTCTTTT
1 AATTAGTTT-TATGTTTAAATCGATTGTCATGCTCAAATACTGCTTCTTTT
26394 AAATCGATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 4 0.10
51 38 0.90
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (51 bp):
AATTAGTTTTATGTTTAAATCGATTGTCATGCTCAAATACTGCTTCTTTTG
Found at i:30890 original size:21 final size:22
Alignment explanation
Indices: 30858--30900 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
30848 TTTATTAACT
*
30858 TTTAATTCTTTT-TTAATTTTA
1 TTTAATTCTTTTATAAATTTTA
30879 TTTAATAT-TTTTATAAATTTTA
1 TTTAAT-TCTTTTATAAATTTTA
30901 ATAATGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTAATTCTTTTATAAATTTTA
Found at i:34482 original size:21 final size:21
Alignment explanation
Indices: 34441--34487 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
34431 TTAATTTTTA
*
34441 ATTTTTTAAACTTTATTTAAT
1 ATTTTTTAAACTTTATATAAT
*
34462 ATTTTTATAAATTTTA-ATAAT
1 ATTTTT-TAAACTTTATATAAT
*
34483 CTTTT
1 ATTTT
34488 AAAAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTTAAACTTTATATAAT
Found at i:36377 original size:27 final size:25
Alignment explanation
Indices: 36343--36405 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
36333 AGATTTTTAT
*
36343 ATTTTTTAAGTTAAATTTGTTTATAC
1 ATTTTTTAAGTTAAATTT-TTCATAC
*
36369 AATTTTTTATTATTTAAATTTTTCATAC
1 -ATTTTTTA--AGTTAAATTTTTCATAC
36397 ATTTTTTAA
1 ATTTTTTAA
36406 TTTTAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
27 16 0.50
28 6 0.19
29 9 0.28
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (25 bp):
ATTTTTTAAGTTAAATTTTTCATAC
Found at i:39238 original size:2 final size:2
Alignment explanation
Indices: 39233--39258 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39223 AACCTTAGAA
39233 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
39259 TTGTGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45546 original size:30 final size:30
Alignment explanation
Indices: 45512--45569 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
45502 AGAATTTCAA
45512 TAAATAA-ATAAAAATAAA-ATTATTAAAATT
1 TAAATAATAT-AAAATAAATATT-TTAAAATT
*
45542 TAAATAATATAATATAAATATTTTAAAA
1 TAAATAATATAAAATAAATATTTTAAAA
45570 AATATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAATAATATAAAATAAATATTTTAAAATT
Found at i:51045 original size:27 final size:28
Alignment explanation
Indices: 51014--51071 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
51004 ACACCCCTTA
51014 GTGCCGCCACTT-GATATTCCTCCATT-G
1 GTGCCGCCACTTCG-TATTCCTCCATTAG
*
51041 GTGCCGCCACTTCGTGTTCCTCCATTAG
1 GTGCCGCCACTTCGTATTCCTCCATTAG
51069 GTG
1 GTG
51072 TCAGGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.33
Consensus pattern (28 bp):
GTGCCGCCACTTCGTATTCCTCCATTAG
Found at i:51941 original size:21 final size:21
Alignment explanation
Indices: 51917--51957 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
51907 GTTAGAAAAC
51917 ATTTATT-TTATCATTTTTAAT
1 ATTTATTATTAT-ATTTTTAAT
*
51938 ATTTTTTATTATATTTTTAA
1 ATTTATTATTATATTTTTAA
51958 AAAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTATTATTATATTTTTAAT
Found at i:53962 original size:26 final size:26
Alignment explanation
Indices: 53899--53948 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53889 AAAAATAATA
53899 ATTAACATTTCCAATGCCAAACTTGT
1 ATTAACATTTCCAATGCCAAACTTGT
*
53925 ATTAACGTTTCCAATGCCAAACTT
1 ATTAACATTTCCAATGCCAAACTT
53949 TGATATGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (26 bp):
ATTAACATTTCCAATGCCAAACTTGT
Found at i:76204 original size:20 final size:20
Alignment explanation
Indices: 76176--76214 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
76166 TTACCCTATA
*
76176 TTATTATATATTTT-TCTTTT
1 TTATAATAT-TTTTCTCTTTT
76196 TTATAATATTTTTCTCTTT
1 TTATAATATTTTTCTCTTT
76215 GTACAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATAATATTTTTCTCTTTT
Found at i:78134 original size:3 final size:3
Alignment explanation
Indices: 78126--78154 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
78116 CAACACAATG
78126 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
78155 TAAAACATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:79088 original size:29 final size:29
Alignment explanation
Indices: 79051--79109 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
79041 AATATAAAAA
79051 AAATAATTAATAATCAAAATAGTATCTTT
1 AAATAATTAATAATCAAAATAGTATCTTT
* * * *
79080 AAATTATTATTTATCAAAATAGTATGTTT
1 AAATAATTAATAATCAAAATAGTATCTTT
79109 A
1 A
79110 GTTAAATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATAATTAATAATCAAAATAGTATCTTT
Found at i:79178 original size:11 final size:11
Alignment explanation
Indices: 79162--79186 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
79152 TTGACACTTA
79162 TTTTTTTAATT
1 TTTTTTTAATT
79173 TTTTTTTAATT
1 TTTTTTTAATT
79184 TTT
1 TTT
79187 ATATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTAATT
Done.