Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012610.1 Kokia drynarioides strain JFW-HI SEQ_127619, 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: 69703
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:8710 original size:217 final size:217
Alignment explanation
Indices: 8335--8769 Score: 834
Period size: 217 Copynumber: 2.0 Consensus size: 217
8325 GCACTAACCT
8335 ACGCATTACAAGTTTTTGGCGCTGTTGTCAGGGATTGTTAACTGCTACCATAGTCATTTTTGTGA
1 ACGCATTACAAGTTTTTGGCGCTGTTGTCAGGGATTGTTAACTGCTACCATAGTCATTTTTGTGA
8400 AATTATTTATTTTCAATTTGGTTTTTATTTCTAACATTACTAACTTATTCTTTTTAATTTTGTGA
66 AATTATTTATTTTCAATTTGGTTTTTATTTCTAACATTACTAACTTATTCTTTTTAATTTTGTGA
* **
8465 TTTTCTTTTCAGGTGTTTATAAGCATAGATCGGATTATCGATTTACTCTCTGTAGACCCTGAAAT
131 TTTTCTTTTCAGGTGCTTATAAGCATAGATCGGATTATCGATTTACTCTCCATAGACCCTGAAAT
8530 TGAGCAAACTTTCAGACAAAGA
196 TGAGCAAACTTTCAGACAAAGA
8552 ACGCATTACAAGTTTTTGGCGCTGTTGTCAGGGATTGTTAACTGCTACCATAGTCATTTTTGTGA
1 ACGCATTACAAGTTTTTGGCGCTGTTGTCAGGGATTGTTAACTGCTACCATAGTCATTTTTGTGA
*
8617 AATTATTTATTTTCAATTTGTTTTTTATTTCTAACATTACTAACTTATTCTTTTTAATTTTGTGA
66 AATTATTTATTTTCAATTTGGTTTTTATTTCTAACATTACTAACTTATTCTTTTTAATTTTGTGA
8682 TTTTCTTTTCAGGTGCTTATAAGCATAGATCGGATTATCGATTTACTCTCCATAGACCCTGAAAT
131 TTTTCTTTTCAGGTGCTTATAAGCATAGATCGGATTATCGATTTACTCTCCATAGACCCTGAAAT
8747 TGAGCAAACTTTCAGACAAAGA
196 TGAGCAAACTTTCAGACAAAGA
8769 A
1 A
8770 GACGTGAATG
Statistics
Matches: 214, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 214 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (217 bp):
ACGCATTACAAGTTTTTGGCGCTGTTGTCAGGGATTGTTAACTGCTACCATAGTCATTTTTGTGA
AATTATTTATTTTCAATTTGGTTTTTATTTCTAACATTACTAACTTATTCTTTTTAATTTTGTGA
TTTTCTTTTCAGGTGCTTATAAGCATAGATCGGATTATCGATTTACTCTCCATAGACCCTGAAAT
TGAGCAAACTTTCAGACAAAGA
Found at i:11912 original size:19 final size:19
Alignment explanation
Indices: 11888--11929 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
11878 CTTTTAGGCG
11888 AATGGCTTTTGGTTTATGC
1 AATGGCTTTTGGTTTATGC
11907 AATGGCTTTTGGTTTATGC
1 AATGGCTTTTGGTTTATGC
11926 AATG
1 AATG
11930 CACCTGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (19 bp):
AATGGCTTTTGGTTTATGC
Found at i:21142 original size:34 final size:34
Alignment explanation
Indices: 21085--21150 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
21075 ATATATATGG
*
21085 AAATGCAATGACAATGTAGATGCAGCGACAATAA
1 AAATGCAATGACAATATAGATGCAGCGACAATAA
* *
21119 AAATGCAATGACATTAATA-ATGCAGGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAGCGACAAT
21151 TATACTATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAGCGACAATAA
Found at i:33515 original size:40 final size:40
Alignment explanation
Indices: 33460--33563 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
33450 GTAACCTAGC
* * * *
33460 AGTGTTTATAATGTCAC-GACTAGTACAATAACAATGTTGT
1 AGTGTTTATAGTGTCACTG-CCAGTACAATAACAATATCGT
* * * *
33500 AGTGTTTACAGTGTCACTGCCAGTCCCATAATAATATCGT
1 AGTGTTTATAGTGTCACTGCCAGTACAATAACAATATCGT
33540 AGTGTTTATAGTGTCACTGCCAGT
1 AGTGTTTATAGTGTCACTGCCAGT
33564 TTAGTGGTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (40 bp):
AGTGTTTATAGTGTCACTGCCAGTACAATAACAATATCGT
Found at i:37846 original size:21 final size:21
Alignment explanation
Indices: 37820--37872 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
37810 GTTTTATGCT
37820 CAACCTCACTCATGCTCGTTA
1 CAACCTCACTCATGCTCGTTA
37841 CAACCTCACTCATGCTCGTTA
1 CAACCTCACTCATGCTCGTTA
37862 CAACCTCACTC
1 CAACCTCACTC
37873 CTATACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.42, G:0.08, T:0.26
Consensus pattern (21 bp):
CAACCTCACTCATGCTCGTTA
Found at i:40582 original size:43 final size:43
Alignment explanation
Indices: 40521--40607 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
40511 GTGCCAAAGA
40521 TAGAAAATTGTCCGATGGCTAAGGTCCTGCATTTGTTGCGGAT
1 TAGAAAATTGTCCGATGGCTAAGGTCCTGCATTTGTTGCGGAT
40564 TAGAAAATTGTCCGATGGCTAAGGTCCTGCATTTGTTGCGGAT
1 TAGAAAATTGTCCGATGGCTAAGGTCCTGCATTTGTTGCGGAT
40607 T
1 T
40608 CTCTATAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
TAGAAAATTGTCCGATGGCTAAGGTCCTGCATTTGTTGCGGAT
Found at i:40823 original size:28 final size:28
Alignment explanation
Indices: 40786--40839 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40776 AGTAACAAGT
* *
40786 ATGACTTTTGGGTCAACAGGGAGTAAGC
1 ATGACCTTTGGGTCAACAAGGAGTAAGC
40814 ATGACCTTTGGGTCAACAAGGAGTAA
1 ATGACCTTTGGGTCAACAAGGAGTAA
40840 ATCGGATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (28 bp):
ATGACCTTTGGGTCAACAAGGAGTAAGC
Found at i:49179 original size:351 final size:351
Alignment explanation
Indices: 48489--49165 Score: 1088
Period size: 351 Copynumber: 1.9 Consensus size: 351
48479 TTTAAATGAA
* * *
48489 TTAGAAGTAAATGTCATATGAACTTGTCATAGTGTGATATAAATGGATTCGATCTAATTACAATT
1 TTAGAAGTAAATGTCATATGAACTTGTCATAGTGTAATATAAATAGATCCGATCTAATTACAATT
48554 TTTACAGATAATCATAGGATGTCTATCTCAAAAAGAGATGAAACTAACGAGGTAAACAATAATGT
66 TTTACAGATAATCATAGGATGTCTATCTCAAAAAGAGATGAAACTAACGAGGTAAACAATAATGT
* ** * * *
48619 CTCGACTAATGATTCTAGGGCTAGTCATGGTGCACTGATACTATCTATGATAGAAAACAAAGTAA
131 CCCGACTAATGATTCTAGGGCTAGTCACAGTGCACTAATACTATCTATGACAGAAAACAAAGCAA
* * *
48684 AGCATATGTTCTTCGAGTTGATGGGATAATAGTTCTCGGAGTTCATAAGAAACTATCCGATAGCA
196 AGAATATGTTATTCGAGTTGATGGGATAATAGTTCTCGGAGTTCATAAGAAACAATCCGATAGCA
*
48749 CCACCTCTTCCACCCCTGTTACACAGCCTGCTGCCTGATCGATAGTGCCTCCAGCTATGCCTCCA
261 CCACCTCTTCCACCCCTGTTACACAGCCTGCTGCCTGATCGATAGTGCCTCCAACTATGCCTCCA
48814 CATCCTCCAGTGGTAAAATAGAAGCG
326 CATCCTCCAGTGGTAAAATAGAAGCG
*
48840 TTAGAAGTAAAT-TCCATATGAACTTGTGATAGTGTAATATAAATAGATCCGATCTAATTACAAT
1 TTAGAAGTAAATGT-CATATGAACTTGTCATAGTGTAATATAAATAGATCCGATCTAATTACAAT
* * *
48904 TTTTATAGATAATCATAGGATGTTTATCTCAAAAAGAGATGAAACTGACGAGGTAAACAATAATG
65 TTTTACAGATAATCATAGGATGTCTATCTCAAAAAGAGATGAAACTAACGAGGTAAACAATAATG
* **
48969 TCCCGACTAATGATTCTAGGGCTAGTCACAGTGCACTAATATTATCTATGACAGAAAATGAAGCA
130 TCCCGACTAATGATTCTAGGGCTAGTCACAGTGCACTAATACTATCTATGACAGAAAACAAAGCA
* * * *
49034 AAGAATATGTTATTTGGGTTGATGGGATAATGGTTCTCGGAGTTCATGAA-AAACAATCTGATAG
195 AAGAATATGTTATTCGAGTTGATGGGATAATAGTTCTCGGAGTTCAT-AAGAAACAATCCGATAG
* *
49098 CACCACCTCTTCCACCCCTGTTACACAGCCTGTTGCCTGATCTATAGTGCCTCCAACTATGCCTC
259 CACCACCTCTTCCACCCCTGTTACACAGCCTGCTGCCTGATCGATAGTGCCTCCAACTATGCCTC
49163 CAC
324 CAC
49166 CTTTTCTAGT
Statistics
Matches: 298, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
350 1 0.00
351 295 0.99
352 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (351 bp):
TTAGAAGTAAATGTCATATGAACTTGTCATAGTGTAATATAAATAGATCCGATCTAATTACAATT
TTTACAGATAATCATAGGATGTCTATCTCAAAAAGAGATGAAACTAACGAGGTAAACAATAATGT
CCCGACTAATGATTCTAGGGCTAGTCACAGTGCACTAATACTATCTATGACAGAAAACAAAGCAA
AGAATATGTTATTCGAGTTGATGGGATAATAGTTCTCGGAGTTCATAAGAAACAATCCGATAGCA
CCACCTCTTCCACCCCTGTTACACAGCCTGCTGCCTGATCGATAGTGCCTCCAACTATGCCTCCA
CATCCTCCAGTGGTAAAATAGAAGCG
Found at i:66040 original size:16 final size:15
Alignment explanation
Indices: 66021--66102 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
66011 TTTCTAAGAT
66021 TATTTTAAAAATATA
1 TATTTTAAAAATATA
* *
66036 TTATTTCAAAAGGTATA
1 -TATTTTAAAA-ATATA
66053 TATTTTTAAAAAT-TA
1 TA-TTTTAAAAATATA
* *
66068 -ATTATCATAAATATA
1 TATT-TTAAAAATATA
66083 TATTTTCAAAAATAT-
1 TATTTT-AAAAATATA
66098 TATTT
1 TATTT
66103 ATCCAAAGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
13 2 0.04
14 7 0.13
15 10 0.19
16 22 0.42
17 11 0.21
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (15 bp):
TATTTTAAAAATATA
Found at i:66057 original size:32 final size:31
Alignment explanation
Indices: 66021--66102 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 31
66011 TTTCTAAGAT
66021 TATTTTAAAAATATATTATTTCA-AAAGGTATA
1 TATTTTAAAAATATATTATTTCATAAA--TATA
66053 TATTTTTAAAAAT-TA--ATTATCATAAATATA
1 TA-TTTTAAAAATATATTATT-TCATAAATATA
*
66083 TATTTTCAAAA-ATATTATTT
1 TATTTTAAAAATATATTATTT
66103 ATCCAAAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
29 10 0.23
30 10 0.23
31 6 0.14
32 7 0.16
33 10 0.23
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (31 bp):
TATTTTAAAAATATATTATTTCATAAATATA
Found at i:66652 original size:16 final size:17
Alignment explanation
Indices: 66622--66654 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
66612 CATATAGCTC
*
66622 TTTTAAAATTTTTAAAA
1 TTTTAAAATTATTAAAA
66639 TTTT-AAATTATTAAAA
1 TTTTAAAATTATTAAAA
66655 GTAAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAAAATTATTAAAA
Found at i:67564 original size:16 final size:16
Alignment explanation
Indices: 67513--67564 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
67503 TATTTTATTC
67513 ATTT-AATTCAAAAAT
1 ATTTAAATTCAAAAAT
* * *
67528 AATAATAATTACAAAAGT
1 ATTTA-AATT-CAAAAAT
67546 ATTTAAATTCAAAAAT
1 ATTTAAATTCAAAAAT
67562 ATT
1 ATT
67565 CATTAAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 8 0.29
18 9 0.32
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTTAAATTCAAAAAT
Found at i:68734 original size:4 final size:4
Alignment explanation
Indices: 68727--68765 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
68717 GAAGGAAAAA
* *
68727 AAAG AAAG AAAA AATAG AAAG AAAG AAAA AAAG AAAG AA
1 AAAG AAAG AAAG AA-AG AAAG AAAG AAAG AAAG AAAG AA
68766 GGAAGAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:68739 original size:13 final size:13
Alignment explanation
Indices: 68721--68762 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
68711 TGAGTTGAAG
68721 GAAAAAAAAGAAA
1 GAAAAAAAAGAAA
*
68734 GAAAAAATAGAAA
1 GAAAAAAAAGAAA
*
68747 GAAAGAAAA-AAA
1 GAAAAAAAAGAAA
68759 GAAA
1 GAAA
68763 GAAGGAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
GAAAAAAAAGAAA
Found at i:68749 original size:17 final size:16
Alignment explanation
Indices: 68722--68765 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
68712 GAGTTGAAGG
68722 AAAAA-AAAGAAAGAA
1 AAAAAGAAAGAAAGAA
68737 AAAATAGAAAGAAAGAA
1 AAAA-AGAAAGAAAGAA
68754 AAAAAGAAAGAA
1 AAAAAGAAAGAA
68766 GGAAGAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 9 0.33
17 14 0.52
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAAGAA
Found at i:69183 original size:20 final size:21
Alignment explanation
Indices: 69142--69184 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
69132 TAATTTACTT
69142 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
69163 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
69183 TA
1 TA
69185 GTAGTAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Done.