Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011938.1 Kokia drynarioides strain JFW-HI SEQ_126936, 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: 36236
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:675 original size:29 final size:29
Alignment explanation
Indices: 606--676 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 29
596 TACTCATAAT
**
606 AAAATCAAACCTTTCAAAATGATCAAATA
1 AAAATCAAATATTTCAAAATGATCAAATA
*** * *
635 AGTGTCAAAATATTTTAAATTGATCAAATA
1 AAAATC-AAATATTTCAAAATGATCAAATA
665 AAAATCAAATAT
1 AAAATCAAATAT
677 ACTCAAATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAATCAAATATTTCAAAATGATCAAATA
Found at i:703 original size:75 final size:75
Alignment explanation
Indices: 617--773 Score: 278
Period size: 75 Copynumber: 2.1 Consensus size: 75
607 AAATCAAACC
*
617 TTTCAAAATGATCAAATAAGTGTCAAAATATTTTAAATTGATCAAATAAAAATCAAATATACTCA
1 TTTCAAAATGATCAAATAAGTGTCAAAACATTTTAAATTGATCAAATAAAAATCAAATATACTCA
682 AATAAAGACT
66 AATAAAGACT
692 TTTCAAAATGATCAAATAAGTGTCAAAACATTTTAAATTGATCAAATAAAAATCAAATATACTCA
1 TTTCAAAATGATCAAATAAGTGTCAAAACATTTTAAATTGATCAAATAAAAATCAAATATACTCA
* **
757 AATGAAGGTT
66 AATAAAGACT
767 TTTCAAA
1 TTTCAAA
774 TGTTAACTAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (75 bp):
TTTCAAAATGATCAAATAAGTGTCAAAACATTTTAAATTGATCAAATAAAAATCAAATATACTCA
AATAAAGACT
Found at i:748 original size:30 final size:31
Alignment explanation
Indices: 691--748 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
681 AAATAAAGAC
***
691 TTTTCAAAATGATCAAATAAGTGTCAAAACA
1 TTTTCAAAATGATCAAATAAAAATCAAAACA
*
722 TTTT-AAATTGATCAAATAAAAATCAAA
1 TTTTCAAAATGATCAAATAAAAATCAAA
749 TATACTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (31 bp):
TTTTCAAAATGATCAAATAAAAATCAAAACA
Found at i:2770 original size:56 final size:56
Alignment explanation
Indices: 2709--2820 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
2699 CATCATCCTT
*
2709 ATCTTTTCTTTTTTTCATTTTAACAAAATAGTTTAATTTCAATTTTAACCCTTTTA
1 ATCTTTTCTTTTGTTCATTTTAACAAAATAGTTTAATTTCAATTTTAACCCTTTTA
2765 ATCTTTTCTTTTGTTCATTTTAACAAAATAGTTTAATTTCAATTTTAACCCTTTTA
1 ATCTTTTCTTTTGTTCATTTTAACAAAATAGTTTAATTTCAATTTTAACCCTTTTA
2821 TTATACTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.29, C:0.14, G:0.03, T:0.54
Consensus pattern (56 bp):
ATCTTTTCTTTTGTTCATTTTAACAAAATAGTTTAATTTCAATTTTAACCCTTTTA
Found at i:3831 original size:23 final size:24
Alignment explanation
Indices: 3785--3844 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
3775 TATTATTTAA
3785 TTTTTAATTAAATATTAAAAATAT
1 TTTTTAATTAAATATTAAAAATAT
* * *
3809 TTTTTTATT-AATATTACATATAT
1 TTTTTAATTAAATATTAAAAATAT
* *
3832 GTTATAATTAAAT
1 TTTTTAATTAAAT
3845 TAAATTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTTAATTAAATATTAAAAATAT
Found at i:9295 original size:56 final size:56
Alignment explanation
Indices: 9223--9391 Score: 295
Period size: 56 Copynumber: 3.0 Consensus size: 56
9213 TATTCTATTG
9223 CCAAGAATAGATCTAGAAGAGAAATTAAACCTTTGAAGAGGTATGTCGAGGCTGAT
1 CCAAGAATAGATCTAGAAGAGAAATTAAACCTTTGAAGAGGTATGTCGAGGCTGAT
*
9279 CCAATAATAGATCTAGAAGAGAAATTAAACCTTTGAAGAGGTATGTCGAGGCTGAT
1 CCAAGAATAGATCTAGAAGAGAAATTAAACCTTTGAAGAGGTATGTCGAGGCTGAT
* *
9335 CCAAGAATAGATCTAGAAGAGAAATTAAA-CTTCTGAAGAGGTATGCCAAGGCTGAT
1 CCAAGAATAGATCTAGAAGAGAAATTAAACCTT-TGAAGAGGTATGTCGAGGCTGAT
9391 C
1 C
9392 TAGTGGCTTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
55 3 0.03
56 105 0.97
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (56 bp):
CCAAGAATAGATCTAGAAGAGAAATTAAACCTTTGAAGAGGTATGTCGAGGCTGAT
Found at i:11032 original size:35 final size:35
Alignment explanation
Indices: 10986--11056 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
10976 ATCCAAATTG
10986 AAGTAGCAATCCTCGATTCTTTTCAGAACTTATCT
1 AAGTAGCAATCCTCGATTCTTTTCAGAACTTATCT
11021 AAGTAGCAATCCTCGATTCTTTTCAGAACTTATCT
1 AAGTAGCAATCCTCGATTCTTTTCAGAACTTATCT
11056 A
1 A
11057 TCTCCTACGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.37
Consensus pattern (35 bp):
AAGTAGCAATCCTCGATTCTTTTCAGAACTTATCT
Found at i:13575 original size:23 final size:24
Alignment explanation
Indices: 13543--13589 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
13533 ACTACCATTT
13543 TTTAAATAAAATAATAA-TAAATA
1 TTTAAATAAAATAATAATTAAATA
* *
13566 TTTAAGTAAAATATTAATTAAATA
1 TTTAAATAAAATAATAATTAAATA
13590 ATATTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTAAATAAAATAATAATTAAATA
Found at i:14295 original size:30 final size:31
Alignment explanation
Indices: 14261--14329 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
14251 CATTTAACAC
* *
14261 AACAGTCACTCA-ATT-TTGAAAATGTGACAA
1 AACAGTCACTAACATTATCGAAAA-GTGACAA
14291 AACAGTCACTAACATTATCGAAAAGTGACAA
1 AACAGTCACTAACATTATCGAAAAGTGACAA
*
14322 AATAGTCA
1 AACAGTCA
14330 TTGAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 11 0.32
31 17 0.50
32 6 0.18
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.23
Consensus pattern (31 bp):
AACAGTCACTAACATTATCGAAAAGTGACAA
Found at i:17602 original size:29 final size:30
Alignment explanation
Indices: 17567--17625 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
17557 TTACGTGTAT
*
17567 AATTGCAC-CAAATGAAAGTTCATGTATAC
1 AATTGCACACAAATCAAAGTTCATGTATAC
*
17596 AATTGCACATTAAATCAAAGTTCATGTATA
1 AATTGCACA-CAAATCAAAGTTCATGTATA
17626 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (30 bp):
AATTGCACACAAATCAAAGTTCATGTATAC
Found at i:17628 original size:29 final size:27
Alignment explanation
Indices: 17562--17628 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
17552 GAGTTTTACG
*
17562 TGTATAATTGCACCAAATGAAAGTTCA
1 TGTATAATTGCACCAAATCAAAGTTCA
*
17589 TGTATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTGCAC--CAAATCAAAGTTCA
17620 TGTATAATT
1 TGTATAATT
17629 TTAATATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 12 0.35
31 17 0.50
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAGTTCA
Found at i:18165 original size:15 final size:15
Alignment explanation
Indices: 18145--18174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18135 GTATTAAAAG
*
18145 TGTATTTAGACCAAT
1 TGTATTTACACCAAT
18160 TGTATTTACACCAAT
1 TGTATTTACACCAAT
18175 ATGTTATTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (15 bp):
TGTATTTACACCAAT
Found at i:19288 original size:33 final size:33
Alignment explanation
Indices: 19245--19340 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
19235 GTGTGTTAGG
* *
19245 GTGTGTATGTATATTGTTTAGAAGCACACGAAC
1 GTGTGAATGTATTTTGTTTAGAAGCACACGAAC
19278 GTGTGAATGTATTTTGTTTAGAAGCACACGAAC
1 GTGTGAATGTATTTTGTTTAGAAGCACACGAAC
19311 GTGTGAATGTATTTTGTTTAGAAGCACACG
1 GTGTGAATGTATTTTGTTTAGAAGCACACG
19341 GGCTGGCACA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.34
Consensus pattern (33 bp):
GTGTGAATGTATTTTGTTTAGAAGCACACGAAC
Found at i:19891 original size:40 final size:40
Alignment explanation
Indices: 19847--19988 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
19837 TTGAGTTGGT
* *
19847 AGTGACACTGTAAACACTGCAATATTATAATTGACCCGAC
1 AGTGACACTGTAAACACTGCAATATTATAACTGAACCGAC
* *
19887 AGTGACACTGTAAACATTGCAATATTATAACTGAACCTAC
1 AGTGACACTGTAAACACTGCAATATTATAACTGAACCGAC
* * ** * ** **
19927 ATTGACACTATAAACACTGCAAGGTTATCACTGAATTGGT
1 AGTGACACTGTAAACACTGCAATATTATAACTGAACCGAC
*
19967 AGTGACACTATAAACACTGCAA
1 AGTGACACTGTAAACACTGCAA
19989 CGTGTCATAC
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (40 bp):
AGTGACACTGTAAACACTGCAATATTATAACTGAACCGAC
Found at i:20091 original size:29 final size:29
Alignment explanation
Indices: 20049--20106 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20039 ACGAATAAGG
*
20049 GTATCACGTCTGCATTTGTAA-TGGTATCT
1 GTATCACGTCTGCATCTGTAACT-GTATCT
*
20078 GTATCATGTCTGCATCTGTAACTGTATCT
1 GTATCACGTCTGCATCTGTAACTGTATCT
20107 CTGACATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (29 bp):
GTATCACGTCTGCATCTGTAACTGTATCT
Found at i:21434 original size:19 final size:19
Alignment explanation
Indices: 21393--21434 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
21383 CTTGAATATC
* *
21393 AAATATTAATTCATATTAT
1 AAATATTAATACACATTAT
21412 AAATATATAATACACATTA-
1 AAATAT-TAATACACATTAT
21431 AAAT
1 AAAT
21435 TGCGGCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTAATACACATTAT
Found at i:23020 original size:63 final size:63
Alignment explanation
Indices: 22953--23085 Score: 205
Period size: 63 Copynumber: 2.1 Consensus size: 63
22943 ATTCAGCACC
* * *
22953 TTAATTGTACTTTTAACAATTTCATCATTGTACTTATAATATTAATTTTTTACTTGGTAGTAT
1 TTAATTGTACTTTTAACAATTTCATCATTGTACATATAATATTAATTTGTTAATTGGTAGTAT
* * *
23016 TTAATTGTACTTTTGACAATTTCATCATTGTACATGTAGTATTAATTTGTTAATTGGTAGTAT
1 TTAATTGTACTTTTAACAATTTCATCATTGTACATATAATATTAATTTGTTAATTGGTAGTAT
23079 TT-ATTGT
1 TTAATTGT
23086 TTATGGCCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
62 5 0.08
63 59 0.92
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (63 bp):
TTAATTGTACTTTTAACAATTTCATCATTGTACATATAATATTAATTTGTTAATTGGTAGTAT
Found at i:24347 original size:45 final size:44
Alignment explanation
Indices: 24260--24346 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
24250 CAAGCTTAAA
24260 CTTTCAACTCCTTAAATAAAAAATATACTGTTGCACAAAAAAAC
1 CTTTCAACTCCTTAAATAAAAAATATACTGTTGCACAAAAAAAC
* *
24304 CTTTCAACTCCTTACATCAAAAATATACTGTTGCACAAAAAAA
1 CTTTCAACTCCTTAAATAAAAAATATACTGTTGCACAAAAAAA
24347 AGCTTTAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.28
Consensus pattern (44 bp):
CTTTCAACTCCTTAAATAAAAAATATACTGTTGCACAAAAAAAC
Found at i:35329 original size:13 final size:13
Alignment explanation
Indices: 35311--35336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35301 TTATTCAGTA
35311 TAGGTAAATTTCG
1 TAGGTAAATTTCG
35324 TAGGTAAATTTCG
1 TAGGTAAATTTCG
35337 AGGACGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TAGGTAAATTTCG
Done.