Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015060.1 Kokia drynarioides strain JFW-HI SEQ_130104, 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: 25062
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:922 original size:60 final size:60
Alignment explanation
Indices: 829--948 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
819 TAATACTTCA
829 TATAGTGTCATCTGAATACTTGACTGATAACTGTTATTATAGGTGAATTCAATCAATGGC
1 TATAGTGTCATCTGAATACTTGACTGATAACTGTTATTATAGGTGAATTCAATCAATGGC
889 TATAGTGTCATCTGAATACTTGACTGATAACTGTTATTATAGGTGAATTCAATCAATGGC
1 TATAGTGTCATCTGAATACTTGACTGATAACTGTTATTATAGGTGAATTCAATCAATGGC
949 AAATACTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (60 bp):
TATAGTGTCATCTGAATACTTGACTGATAACTGTTATTATAGGTGAATTCAATCAATGGC
Found at i:2313 original size:43 final size:43
Alignment explanation
Indices: 2247--2417 Score: 236
Period size: 43 Copynumber: 4.0 Consensus size: 43
2237 TTTACAGTTA
* * * *
2247 TTTAGCGGCTTTTATGGGAAAAGCGTCGCTAAAGACCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
2290 TTTAGCGGCGTTTGTGCGG-AAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGACCATGTTC
*
2333 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * **
2376 TTTAGCCGCGTTCGTGGGAAAATCATCGCTAAAGACCATGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTT
2418 TTATAGCAGC
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
42 2 0.02
43 111 0.97
44 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:2466 original size:15 final size:15
Alignment explanation
Indices: 2446--2476 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2436 TCATAAACGC
2446 CGTTATCTTTAGCGA
1 CGTTATCTTTAGCGA
2461 CGTTATCTTTAGCGA
1 CGTTATCTTTAGCGA
2476 C
1 C
2477 ATTAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (15 bp):
CGTTATCTTTAGCGA
Found at i:7029 original size:18 final size:19
Alignment explanation
Indices: 7008--7046 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
6998 TTTTTTGAAA
7008 TATATATATTTTA-TTATT
1 TATATATATTTTATTTATT
*
7026 TATATTTATTTTATTTATT
1 TATATATATTTTATTTATT
7045 TA
1 TA
7047 ATCTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATATATATTTTATTTATT
Found at i:8783 original size:17 final size:19
Alignment explanation
Indices: 8757--8797 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
8747 TTATACTGAA
*
8757 TTTATTTTG-TTTTA-GTG
1 TTTATATTGATTTTAGGTG
8774 TTTATATTGTATTTTAGGTG
1 TTTATATTG-ATTTTAGGTG
8794 TTTA
1 TTTA
8798 CTCTTGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (19 bp):
TTTATATTGATTTTAGGTG
Found at i:12242 original size:23 final size:23
Alignment explanation
Indices: 12214--12293 Score: 133
Period size: 23 Copynumber: 3.5 Consensus size: 23
12204 CGTCCATCCT
*
12214 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
*
12237 TGCTGATTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
*
12260 TGCTGATTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
12283 TGCTGACTGGA
1 TGCTGACTGGA
12294 TGCCACGTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAGC
Found at i:15935 original size:18 final size:17
Alignment explanation
Indices: 15912--15963 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
15902 AATAGAAATA
15912 AAATAAAATAAATAATCG
1 AAATAAAATAAATAAT-G
*
15930 AAAT-AAATTAATAATG
1 AAATAAAATAAATAATG
15946 AAGTATAAAATTAAATAA
1 AA--ATAAAA-TAAATAA
15964 ATAAAACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 10 0.36
18 6 0.21
19 3 0.11
20 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (17 bp):
AAATAAAATAAATAATG
Found at i:23461 original size:29 final size:29
Alignment explanation
Indices: 23418--23666 Score: 89
Period size: 29 Copynumber: 8.4 Consensus size: 29
23408 CTTTAGGGGC
23418 AAAATGGTAATTTTTAGAAAGTTC-AGCGTCA
1 AAAAT-GTAA-TTTTAGAAAGTTCAAG-GTCA
* *
23449 AAAATGTAATTTTTGGAAGTTCAAGGTCA
1 AAAATGTAATTTTAGAAAGTTCAAGGTCA
* * ** *
23478 AAAATGGAATTTTTAGACA-TTCGGGGGC-
1 AAAATGTAA-TTTTAGAAAGTTCAAGGTCA
* **
23506 AAAATGGTAATTTTTGGAAAAATCGAA-GTCA
1 AAAAT-GTAA-TTTTAGAAAGTTC-AAGGTCA
* * * * *
23537 AAAATGGAATTTTTGGAAGTTCGAGTTCA
1 AAAATGTAATTTTAGAAAGTTCAAGGTCA
* * * *
23566 AAAATAG-AATTTTTGTGAAGTTTAGGGGTC-
1 AAAAT-GTAATTTTAG-AAAGTTCA-AGGTCA
* * * * *
23596 AAAATATAATTTTTGGATGTTC-GGGATCA
1 AAAATGTAATTTTAGAAAGTTCAAGG-TCA
* * * *
23625 AAAATGTAATTTTTGGAAGTTCGAGGACA
1 AAAATGTAATTTTAGAAAGTTCAAGGTCA
*
23654 AAAATGGAATTTT
1 AAAATGTAATTTT
23667 TAGACATTAG
Statistics
Matches: 169, Mismatches: 35, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.02
28 8 0.05
29 104 0.62
30 41 0.24
31 13 0.08
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAGTTCAAGGTCA
Found at i:23506 original size:88 final size:87
Alignment explanation
Indices: 23389--23915 Score: 457
Period size: 88 Copynumber: 6.0 Consensus size: 87
23379 ACCCGAGGAT
* *
23389 AAAATGGTAATTTTTA-ACACTTTA-GGGGCAAAATGGTAATTTTTAGAAAGTTC-AGCGTCAAA
1 AAAATGG-AATTTTTAGACA-GTTAGGGGGCAAAAT-ATAATTTTT-GAAAGTTCGAG-GTCAAA
* *
23451 AATGTAATTTTTGGAAGTTCAAGGTCA
61 AATGGAATTTTTGGAAGTTCGAGGTCA
* * ** *
23478 AAAATGGAATTTTTAGACA-TTCGGGGGCAAAATGGTAATTTTTGGAAAAATCGAAGTCAAAAAT
1 AAAATGGAATTTTTAGACAGTTAGGGGGCAAAAT-ATAATTTTT-GAAAGTTCGAGGTCAAAAAT
*
23542 GGAATTTTTGGAAGTTCGAGTTCA
64 GGAATTTTTGGAAGTTCGAGGTCA
* * * * *
23566 AAAATAGAATTTTTGTGA-AGTTTAGGGGTCAAAATATAATTTTTGGATGTTCG-GGATCAAAAA
1 AAAATGGAATTTTT-AGACAG-TTAGGGGGCAAAATATAATTTTTGAAAGTTCGAGG-TCAAAAA
* *
23629 TGTAATTTTTGGAAGTTCGAGGACA
63 TGGAATTTTTGGAAGTTCGAGGTCA
** *
23654 AAAATGGAATTTTTAGACA-TTAGGGGGCAAAATGATAATTTTTGGAAAAATCGAGG-CTAGAAA
1 AAAATGGAATTTTTAGACAGTTAGGGGGCAAAAT-ATAATTTTT-GAAAGTTCGAGGTC-AAAAA
* *
23717 TGGAGTTTTTGGAAGTTCGGGGTCA
63 TGGAATTTTTGGAAGTTCGAGGTCA
* * * * * *
23742 AAAATAGAATTTTTGTGA-AGTTTGGGGCTCAAAATATAATTTTTGGAAGTTCGAGATCAAAAAT
1 AAAATGGAATTTTT-AGACAGTTAGGGG-GCAAAATATAATTTTTGAAAGTTCGAGGTCAAAAAT
*
23806 GTAATTTTTGGAAGTTCGAGGGT-A
64 GGAATTTTTGGAAGTTCGA-GGTCA
* * * * * * * *
23830 AAAATGTACTTTTTGGAAAGTTCGAGGTCTAAAATGTAATTATTTG-AAGTTCGAGGGT-AAAAA
1 AAAATGGAATTTTTAGACAGTTAGGGGGC-AAAATATAATT-TTTGAAAGTTCGA-GGTCAAAAA
23893 TGGAATTTTTGGAAAGTTCGAGG
63 TGGAATTTTTGG-AAGTTCGAGG
23916 GTTAAAATAT
Statistics
Matches: 362, Mismatches: 54, Indels: 45
0.79 0.12 0.10
Matches are distributed among these distances:
86 13 0.04
87 19 0.05
88 254 0.70
89 58 0.16
90 18 0.05
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (87 bp):
AAAATGGAATTTTTAGACAGTTAGGGGGCAAAATATAATTTTTGAAAGTTCGAGGTCAAAAATGG
AATTTTTGGAAGTTCGAGGTCA
Found at i:23658 original size:176 final size:176
Alignment explanation
Indices: 23446--23915 Score: 637
Period size: 176 Copynumber: 2.7 Consensus size: 176
23436 AAGTTCAGCG
* *
23446 TCAAAAATGTAATTTTTGGAAGTTCAAGGTCAAAAATGGAATTTTTAGACATTCGGGGGCAAAAT
1 TCAAAAATGTAATTTTTGGAAGTTCGAGGACAAAAATGGAATTTTTAGACATTCGGGGGCAAAAT
*
23511 GGTAATTTTTGGAAAAATCGAAGTCAAAAATGGAATTTTTGGAAGTTCGAGTTCAAAAATAGAAT
66 GGTAATTTTTGGAAAAATCGAAGTCAAAAATGGAATTTTTGGAAGTTCGAGGTCAAAAATAGAAT
* *
23576 TTTTGTGAAGTTTAGGGG-TCAAAATATAATTTTTGGATGTTCGGGA
131 TTTTGTGAAGTTT-GGGGCTCAAAATATAATTTTTGGAAGTTCGAGA
*
23622 TCAAAAATGTAATTTTTGGAAGTTCGAGGACAAAAATGGAATTTTTAGACATTAGGGGGCAAAAT
1 TCAAAAATGTAATTTTTGGAAGTTCGAGGACAAAAATGGAATTTTTAGACATTCGGGGGCAAAAT
* * * * *
23687 GATAATTTTTGGAAAAATCG-AGGCTAGAAATGGAGTTTTTGGAAGTTCGGGGTCAAAAATAGAA
66 GGTAATTTTTGGAAAAATCGAAGTC-AAAAATGGAATTTTTGGAAGTTCGAGGTCAAAAATAGAA
23751 TTTTTGTGAAGTTTGGGGCTCAAAATATAATTTTTGGAAGTTCGAGA
130 TTTTTGTGAAGTTTGGGGCTCAAAATATAATTTTTGGAAGTTCGAGA
** * * * * * *
23798 TCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTACTTTTTGGAAAGTTCGAGGTCTAAA
1 TCAAAAATGTAATTTTTGGAAGTTCGAGGACAAAAATGGAATTTTTAGACA-TTCGGGGGC-AAA
** *
23863 AT-GTAATTATTT-G-AAGTTCGAGGGT-AAAAATGGAATTTTTGGAAAGTTCGAGG
64 ATGGTAATT-TTTGGAAAAATCGA-AGTCAAAAATGGAATTTTTGG-AAGTTCGAGG
23916 GTTAAAATAT
Statistics
Matches: 258, Mismatches: 28, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
175 7 0.03
176 221 0.86
177 21 0.08
178 9 0.03
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.33
Consensus pattern (176 bp):
TCAAAAATGTAATTTTTGGAAGTTCGAGGACAAAAATGGAATTTTTAGACATTCGGGGGCAAAAT
GGTAATTTTTGGAAAAATCGAAGTCAAAAATGGAATTTTTGGAAGTTCGAGGTCAAAAATAGAAT
TTTTGTGAAGTTTGGGGCTCAAAATATAATTTTTGGAAGTTCGAGA
Found at i:23923 original size:59 final size:60
Alignment explanation
Indices: 23418--23922 Score: 399
Period size: 59 Copynumber: 8.6 Consensus size: 60
23408 CTTTAGGGGC
* * *
23418 AAAATGGTAATTTTTAGAAAGTTC-AGCGTCAAAAATGTAATTTTTGGAAGTTC-AAGGTCA
1 AAAATGG-AATTTTTGGAAAGTTCGAGGGTCAAAAATGTAATTTTTGGAAGTTCGAGGGT-A
* * * ** *
23478 AAAATGGAATTTTTAGACA-TTCG-GGGGC-AAAATGGTAATTTTTGGAAAAATCGA-AGTCA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAAT-GTAATTTTTGG-AAGTTCGAGGGT-A
* * *
23537 AAAATGGAATTTTTGG-AAGTTCGA-GTTCAAAAATAG-AATTTTTGTGAAGTT-TAGGGGTC
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAAT-GTAATTTTTG-GAAGTTCGA-GGGTA
** * * **
23596 AAAATATAATTTTTGG-ATGTTCG-GGATCAAAAATGTAATTTTTGGAAGTTCGAGGACA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAATGTAATTTTTGGAAGTTCGAGGGTA
* * * * ** *
23654 AAAATGGAATTTTTAGACA-TTAG-GGGGC-AAAATGATAATTTTTGGAAAAATCGAGGCTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAATG-TAATTTTTGG-AAGTTCGAGGGTA
* * * *
23713 GAAATGGAGTTTTTGG-AAGTTCG-GGGTCAAAAATAG-AATTTTTGTGAAGTTTG-GGGCTC
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAAT-GTAATTTTTG-GAAGTTCGAGGG-TA
** *
23772 AAAATATAATTTTTGG-AAGTTCGA-GATCAAAAATGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAATGTAATTTTTGGAAGTTCGAGGGTA
* * *
23830 AAAATGTACTTTTTGGAAAGTTCGA-GGTCTAAAATGTAATTATTT-GAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAATGTAATT-TTTGGAAGTTCGAGGGTA
*
23889 AAAATGGAATTTTTGGAAAGTTCGAGGGTTAAAA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAA
23923 TATGATTTTC
Statistics
Matches: 356, Mismatches: 62, Indels: 54
0.75 0.13 0.11
Matches are distributed among these distances:
57 11 0.03
58 83 0.23
59 229 0.64
60 32 0.09
61 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAAGTTCGAGGGTCAAAAATGTAATTTTTGGAAGTTCGAGGGTA
Done.