Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004825.1 Kokia drynarioides strain JFW-HI SEQ_118467, 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: 16934
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6270 original size:25 final size:23
Alignment explanation
Indices: 6222--6270 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
6212 AGCTTAATAA
*
6222 TTGAGTATTATTATATATTTAAT
1 TTGAGTATTATTATATATTAAAT
6245 TTGATGTATTTATT-TATGATTAAAT
1 TTGA-GTA-TTATTATAT-ATTAAAT
6270 T
1 T
6271 ATTGCAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (23 bp):
TTGAGTATTATTATATATTAAAT
Found at i:7648 original size:29 final size:28
Alignment explanation
Indices: 7616--7789 Score: 93
Period size: 29 Copynumber: 6.0 Consensus size: 28
7606 TTTTTAGACA
7616 TTCGAGGGTAAAAGGGAAATTTT-GAGAG
1 TTCGAGGGTAAAAGGGAAATTTTGGA-AG
* * *
7644 TTTCGAGGTTGAAAATGGAGATTTTGGAAG
1 -TTCGAGGGT-AAAAGGGAAATTTTGGAAG
* * *
7674 TTCGAGGGCAAAAATGGAATTTTTGGAAG
1 TTCGAGGG-TAAAAGGGAAATTTTGGAAG
* * * *
7703 TTTTGA-GGTAAAAAATGGCATTTTTGGAAG
1 -TTCGAGGGT--AAAAGGGAAATTTTGGAAG
* *
7733 TTCGA-GGTCGAAAATGGAGATTTTGGAAG
1 TTCGAGGGT--AAAAGGGAAATTTTGGAAG
* * * *
7762 TTCAAGGGCAAAAATGGAATTTTTGGAA
1 TTCGAGGG-TAAAAGGGAAATTTTGGAA
7790 TTTTTGGAAG
Statistics
Matches: 117, Mismatches: 20, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
29 77 0.66
30 38 0.32
31 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.30
Consensus pattern (28 bp):
TTCGAGGGTAAAAGGGAAATTTTGGAAG
Found at i:7711 original size:59 final size:59
Alignment explanation
Indices: 7567--8157 Score: 384
Period size: 59 Copynumber: 9.8 Consensus size: 59
7557 CCGAGGGTAG
* * * *
7567 AATGGTAATTTTGGGAAATTTTG-GGGTTTAAAAATGGAATTTTTAGACA-TTCGAGGGT-AA
1 AATGG-AATTTTTGGAAGTTTTGAGGG--TAAAAATGGAATTTTTGGA-AGTTCGAGGTTAAA
* * * * * **
7627 AAGGGAAATTTT-GAGAGTTTCGAGGTTGAAAATGGAGA-TTTTGGAAGTTCGAGGGCAAA
1 AATGGAATTTTTGGA-AGTTTTGAGGGTAAAAATGGA-ATTTTTGGAAGTTCGAGGTTAAA
* **
7686 AATGGAATTTTTGGAAGTTTTGA-GGTAAAAAATGGCATTTTTGGAAGTTCGAGGTCGAA
1 AATGGAATTTTTGGAAGTTTTGAGGGT-AAAAATGGAATTTTTGGAAGTTCGAGGTTAAA
** * *
7745 AATGGAGA-TTTTGGAAG-TTCAAGGGCAAAAATGGAATTTTTGGAATTTTTGGAAGTTTTGAGG
1 AATGGA-ATTTTTGGAAGTTTTGAGGG--TAAA---AA----TGGAATTTTTGGAAG-TTCGAGG
*
7808 TCAAA
55 TTAAA
* * **
7813 AATGGCATTTTTGGAAG-TTTGAGGGTAAAAATGGAATTTTTGAAAGTTTTATGGTTAAA
1 AATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGTTCGA-GGTTAAA
* ** * * *
7872 AATGGGATTTTTTGGAAGTTCGGA-GGTAAAAATAGAATTTTTGAAAGTTTCGAGGTAAAA
1 AAT-GGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAG-TTCGAGGTTAAA
* *
7932 AATGAGATTTTTTGGAAG-TTTGGGGGT-AAAATGGAATTTTTGGAAGTTTCGAGGTTAAA
1 AATG-GAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAG-TTCGAGGTTAAA
* * * * * *
7991 AATGGGATTTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGGAGTTTGGGGGGTAAA
1 AATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAG-TTCGAGGTTAAA
* * * ** * * *
8050 AATAGAATTTTTAGAAGTTTT-AGGGTTTAAAATGGGGTTTTTAGAAGTT-TAGGGGTAAA
1 AATGGAATTTTTGGAAGTTTTGAGGG-TAAAAATGGAATTTTTGGAAGTTCGA-GGTTAAA
* * * ***
8109 AATAGAATTTTTTGAAGTTTCGAGGGTAAAAACAAAATTTTTGGAAGTT
1 AATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGTT
8158 TTAGGACCTC
Statistics
Matches: 427, Mismatches: 72, Indels: 65
0.76 0.13 0.12
Matches are distributed among these distances:
57 1 0.00
58 53 0.12
59 222 0.52
60 93 0.22
61 6 0.01
63 4 0.01
66 3 0.01
67 15 0.04
68 30 0.07
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
AATGGAATTTTTGGAAGTTTTGAGGGTAAAAATGGAATTTTTGGAAGTTCGAGGTTAAA
Found at i:7719 original size:30 final size:29
Alignment explanation
Indices: 7595--8158 Score: 339
Period size: 30 Copynumber: 18.8 Consensus size: 29
7585 TTTTGGGGTT
*
7595 TAAAAATGGAATTTTTAGACA--TTCGAGGG
1 TAAAAATGGAATTTTTGGA-AGTTTCGA-GG
* *
7624 T-AAAAGGGAAATTTT-GAGAGTTTCGAGG
1 TAAAAATGGAATTTTTGGA-AGTTTCGAGG
*
7652 TTGAAAATGGAGA-TTTTGGAAG-TTCGAGGG
1 -TAAAAATGGA-ATTTTTGGAAGTTTCGA-GG
* *
7682 CAAAAATGGAATTTTTGGAAGTTTTGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGG
*
7711 TAAAAAATGGCATTTTTGGAAG-TTCGAGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGAGG
* *
7740 TCGAAAATGGAGA-TTTTGGAAG-TTCAAGGG
1 T-AAAAATGGA-ATTTTTGGAAGTTTCGA-GG
* *
7770 CAAAAATGGAATTTTTGGAATTTTTGGAAGTTTTGAGG
1 --TAAA---AA----TGGAATTTTTGGAAGTTTCGAGG
* ** ***
7808 TCAAAAATGGCATTTTTGGAAGTTT-GAGGG
1 TAAAAATGGAATTTTT-GGAAGTTTCGA-GG
* *
7838 TAAAAATGGAATTTTTGAAAGTTT-TATGG
1 TAAAAATGGAATTTTTGGAAGTTTCGA-GG
*
7867 TTAAAAATGGGATTTTTTGGAAG-TTCGGAGG
1 -TAAAAAT-GGAATTTTTGGAAGTTTC-GAGG
* *
7898 TAAAAATAGAATTTTTGAAAGTTTCGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGG
* * *
7927 TAAAAAATGAGATTTTTTGGAAGTTTGGGGG
1 T-AAAAATG-GAATTTTTGGAAGTTTCGAGG
7958 T-AAAATGGAATTTTTGGAAGTTTCGAGG
1 TAAAAATGGAATTTTTGGAAGTTTCGAGG
*
7986 TTAAAAATGGGATTTTTGGAAG-TTCGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTTCGA-GG
* * *
8016 TAAAAATGGAATTTTTGGGAGTTTGGGGGG
1 TAAAAATGGAATTTTTGGAAGTTT-CGAGG
* * *
8046 TAAAAATAGAATTTTTAGAAGTTT-TAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGA-GG
* ** * * *
8075 TTTAAAATGGGGTTTTTAGAAGTTTAGGGG
1 -TAAAAATGGAATTTTTGGAAGTTTCGAGG
* *
8105 TAAAAATAGAATTTTTTGAAGTTTCGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGA-GG
***
8135 TAAAAACAAAATTTTTGGAAGTTT
1 TAAAAATGGAATTTTTGGAAGTTT
8159 TAGGACCTCC
Statistics
Matches: 420, Mismatches: 74, Indels: 81
0.73 0.13 0.14
Matches are distributed among these distances:
27 3 0.01
28 33 0.08
29 144 0.34
30 176 0.42
31 38 0.09
32 1 0.00
33 2 0.00
34 2 0.00
36 2 0.00
37 1 0.00
38 15 0.04
39 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGAGG
Found at i:7815 original size:68 final size:67
Alignment explanation
Indices: 7722--7854 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 67
7712 AAAAAATGGC
*
7722 ATTTTTGGAAGTTCGAGGTCGAAAATGG-AGATTTTGGAAGTTCAAGGGCAAAAATGGAATTTTT
1 ATTTTTGGAAGTTCGAGGTCAAAAATGGCA-ATTTTGGAAGTTCAAGGGCAAAAATGGAATTTTT
7786 GGA
65 GGA
* * ** *
7789 ATTTTTGGAAGTTTTGAGGTCAAAAATGGCATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTT
1 ATTTTTGGAAG-TTCGAGGTCAAAAATGGCAATTTTGGAAGTTCAAGGGCAAAAATGGAATTTTT
7854 G
65 G
7855 AAAGTTTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
67 11 0.19
68 46 0.79
69 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (67 bp):
ATTTTTGGAAGTTCGAGGTCAAAAATGGCAATTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTG
GA
Found at i:7823 original size:39 final size:38
Alignment explanation
Indices: 7753--7828 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
7743 AAAATGGAGA
7753 TTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGAAT
1 TTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGAAT
** * *
7791 TTTTGGAAGTTTTGAGGTCAAAAATGGCATTTTTGGAA
1 TTTTGGAAG-TTCAAGGGCAAAAATGGAATTTTTGGAA
7829 GTTTGAGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 9 0.27
39 24 0.73
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (38 bp):
TTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGAAT
Found at i:8052 original size:89 final size:88
Alignment explanation
Indices: 7785--8158 Score: 373
Period size: 89 Copynumber: 4.2 Consensus size: 88
7775 ATGGAATTTT
* * * *
7785 TGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGCATTTTTGGAAGTTTGAGGGTAAAAATGGAAT
1 TGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAAT
* ** *
7850 TTTTGAAAGTTTTATGGTTAAAAA
66 TTTTGGAAG-TTTGGGGGTAAAAA
* * * *
7874 TGGGATTTTTTGGAAG-TTCGGAGG-TAAAAATAGAATTTTTGAAAGTTTCGA-GGTAAAAAATG
1 T-GGAATTTTTGGAAGTTTC-GAGGTTAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAAATG
*
7936 AGATTTTTTGGAAGTTTGGGGGT-AAAA
62 -GAATTTTTGGAAGTTTGGGGGTAAAAA
7963 TGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAAT
1 TGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAAT
*
8028 TTTTGGGAGTTTGGGGGGTAAAAA
66 TTTTGGAAGTTT-GGGGGTAAAAA
* * * * * * * *
8052 TAGAATTTTTAGAAGTTT-TAGGGTTTAAAATGGGGTTTTTAGAAGTT-TAGGGGTAAAAATAGA
1 TGGAATTTTTGGAAGTTTCGA-GGTTAAAAATGGGATTTTTGGAAGTTCGA-GGGTAAAAATGGA
* *
8115 ATTTTTTGAAGTTTCGAGGGTAAAAA
64 ATTTTTGGAAGTTT-GGGGGTAAAAA
***
8141 CAAAATTTTTGGAAGTTT
1 TGGAATTTTTGGAAGTTT
8159 TAGGACCTCC
Statistics
Matches: 240, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
87 14 0.06
88 37 0.15
89 144 0.60
90 34 0.14
91 11 0.05
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (88 bp):
TGGAATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAAT
TTTTGGAAGTTTGGGGGTAAAAA
Found at i:11167 original size:55 final size:55
Alignment explanation
Indices: 11083--11203 Score: 197
Period size: 55 Copynumber: 2.2 Consensus size: 55
11073 TAACTAGTGG
* * *
11083 CCATGAGTGGCGCTCGGGATAACACTATGGACATGCGGGATTATTTGATTAGCGA
1 CCATGAGTGGCGCTCGGGATAACACTATGGACATCCGGGATTATTTGACTAACGA
*
11138 CCATGAGTGGCGCTTGGGATAACACTATGGACATCCGGGATTATTTGACTAACGA
1 CCATGAGTGGCGCTCGGGATAACACTATGGACATCCGGGATTATTTGACTAACGA
*
11193 CCATGACTGGC
1 CCATGAGTGGC
11204 ACGAGACTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (55 bp):
CCATGAGTGGCGCTCGGGATAACACTATGGACATCCGGGATTATTTGACTAACGA
Found at i:14458 original size:30 final size:30
Alignment explanation
Indices: 14422--14478 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
14412 ATGTATACAA
14422 TAACGAACTTAATCTCTTTCAATTCTCTAG
1 TAACGAACTTAATCTCTTTCAATTCTCTAG
14452 TAACGAACTTAATCTCTTTCAATTCTC
1 TAACGAACTTAATCTCTTTCAATTCTC
14479 CTGACTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (30 bp):
TAACGAACTTAATCTCTTTCAATTCTCTAG
Found at i:14547 original size:24 final size:24
Alignment explanation
Indices: 14512--14605 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
14502 CAGACAATAT
* *
14512 TTAGC-CTATACGAGCCTAGAATGT
1 TTAGCTCT-TACGAGCCCAGAATGG
* *
14536 TTAGCTCCTACGAGCCCAGAACGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
14560 TTAGCTCTTACGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
14584 TTAGCTCTTACAAGCCCAGAAT
1 TTAGCTCTTACGAGCCCAGAAT
14606 CAGAATAACG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
24 59 0.98
25 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:14572 original size:48 final size:48
Alignment explanation
Indices: 14512--14604 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
14502 CAGACAATAT
* *
14512 TTAGCCTATACGAGCCTAGAATGTTTAGCTCCTACGAGCCCAGAACGG
1 TTAGCCTATACGAGCCTAGAATGGTTAGCTCCTACAAGCCCAGAACGG
*
14560 TTAGCTCT-TACGAGCCTAGAATGGTTAGCTCTTACAAGCCCAGAA
1 TTAGC-CTATACGAGCCTAGAATGGTTAGCTCCTACAAGCCCAGAA
14605 TCAGAATAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.95
49 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (48 bp):
TTAGCCTATACGAGCCTAGAATGGTTAGCTCCTACAAGCCCAGAACGG
Done.