Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014513.1 Kokia drynarioides strain JFW-HI SEQ_129552, 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: 94703
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 230 characters in sequence are not A, C, G, or T
Found at i:14483 original size:16 final size:16
Alignment explanation
Indices: 14462--14496 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14452 ACAAACAAAA
14462 AAAAC-ATATAAAATTT
1 AAAACAATAT-AAATTT
14478 AAAACAATATAAATTT
1 AAAACAATATAAATTT
14494 AAA
1 AAA
14497 TCGACTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAACAATATAAATTT
Found at i:15771 original size:25 final size:23
Alignment explanation
Indices: 15731--15779 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
15721 TTGATCAGCG
*
15731 TTTTTTTATTTATTTACAATTTA
1 TTTTTTGATTTATTTACAATTTA
*
15754 TTTTTTGATTTTAGTTTACTATTTA
1 TTTTTTGA-TTTA-TTTACAATTTA
15779 T
1 T
15780 ACGTTGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTTGATTTATTTACAATTTA
Found at i:25609 original size:14 final size:15
Alignment explanation
Indices: 25590--25624 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25580 TTTTTGGAAG
*
25590 AGGAAAAG-AGAGAA
1 AGGAAAAGAAAAGAA
25604 AGGAAAAGAAAAGAA
1 AGGAAAAGAAAAGAA
25619 AGGAAA
1 AGGAAA
25625 GGGTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AGGAAAAGAAAAGAA
Found at i:27828 original size:16 final size:17
Alignment explanation
Indices: 27807--27838 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27797 TTACTCTTAT
27807 AATTAT-AAATACATAA
1 AATTATAAAATACATAA
27823 AATTATAAAATACATA
1 AATTATAAAATACATA
27839 TGTAAATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTATAAAATACATAA
Found at i:28327 original size:61 final size:60
Alignment explanation
Indices: 28234--28397 Score: 197
Period size: 61 Copynumber: 2.7 Consensus size: 60
28224 TTGGTATCTA
* *
28234 AATTTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTTACCCAATTTGGA-ACTTG
1 AATTTGACATTTTTTTTCCAATTTGGTACCTAAACTTTTTTTGACCCAATTT-GATACTTG
* * *
28294 AATTTGACACTTTTTTTTCCAATTTGGTACCTAATCTTTTTCTGGCCCAATTTGATACTTG
1 AATTTGACA-TTTTTTTTCCAATTTGGTACCTAAACTTTTTTTGACCCAATTTGATACTTG
* ** *
28355 AACTTGACATTTTTTCCCCTAATTTGGTATCTAAGA-TTTTTTT
1 AATTTGACATTTTTTTTCC-AATTTGGTACCTAA-ACTTTTTTT
28398 AGATTCAATT
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
60 19 0.21
61 70 0.79
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.49
Consensus pattern (60 bp):
AATTTGACATTTTTTTTCCAATTTGGTACCTAAACTTTTTTTGACCCAATTTGATACTTG
Found at i:32624 original size:21 final size:22
Alignment explanation
Indices: 32582--32626 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
32572 ATGCCATTAG
* *
32582 GGTTCAAATGGAAAGAGAAAAT
1 GGTTCAAATCGAAAAAGAAAAT
*
32604 GGTTC-AATCGAAAAAGGAAAT
1 GGTTCAAATCGAAAAAGAAAAT
32625 GG
1 GG
32627 GTGTTTGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.47, C:0.07, G:0.29, T:0.18
Consensus pattern (22 bp):
GGTTCAAATCGAAAAAGAAAAT
Found at i:41351 original size:40 final size:40
Alignment explanation
Indices: 41293--41368 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
41283 AGCAACGAGC
* *
41293 GTTTCAGGCACTTTGTAACCTCGCCTGGTAAGTAGCCATA
1 GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGCCATA
*
41333 GTTTCAGTCACTTGGTAACCTCACCTGGTAAGTAGC
1 GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGC
41369 TCATTGGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.30
Consensus pattern (40 bp):
GTTTCAGGCACTTGGTAACCTCACCTGGTAAGTAGCCATA
Found at i:47713 original size:2 final size:2
Alignment explanation
Indices: 47706--47730 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47696 TAGTCATCAT
47706 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
47731 TAGTGGGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48375 original size:14 final size:14
Alignment explanation
Indices: 48358--48385 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48348 TAATATTATG
48358 TTGTTATTATTTTA
1 TTGTTATTATTTTA
48372 TTGTTATTATTTTA
1 TTGTTATTATTTTA
48386 ATATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
TTGTTATTATTTTA
Found at i:49401 original size:35 final size:35
Alignment explanation
Indices: 49350--49419 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
49340 TAAACTCGTA
*
49350 TCATCATAGCAAATAACCCAAGATCTCCCTGGTCC
1 TCATCATAGCAAATAACCCAAGATCTCCCAGGTCC
* * *
49385 TCATTATAGCAAATAACCCTAGATTTCCCAGGTCC
1 TCATCATAGCAAATAACCCAAGATCTCCCAGGTCC
49420 CAACTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.26
Consensus pattern (35 bp):
TCATCATAGCAAATAACCCAAGATCTCCCAGGTCC
Found at i:51056 original size:39 final size:39
Alignment explanation
Indices: 51013--51091 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
51003 ATATATAAAG
51013 TAAGTTTTGAAAATCGAAACGCTTACAGCTATGACTAAC
1 TAAGTTTTGAAAATCGAAACGCTTACAGCTATGACTAAC
51052 TAAGTTTTGAAAATCGAAACGCTTACAGCTATGACTAAC
1 TAAGTTTTGAAAATCGAAACGCTTACAGCTATGACTAAC
51091 T
1 T
51092 TAAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (39 bp):
TAAGTTTTGAAAATCGAAACGCTTACAGCTATGACTAAC
Found at i:57496 original size:16 final size:16
Alignment explanation
Indices: 57453--57503 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
57443 ATTCAAAATC
*
57453 TAATTTAATAAAAATAT
1 TAATTT-ATTAAAATAT
*
57470 TATTTTATTAAAATAT
1 TAATTTATTAAAATAT
57486 TAAATTT-TTAATAATAT
1 T-AATTTATTAA-AATAT
57503 T
1 T
57504 TTATCTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTTATTAAAATAT
Found at i:58807 original size:9 final size:10
Alignment explanation
Indices: 58777--58805 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
58767 ATATTTATTG
58777 ATTTTAATAA
1 ATTTTAATAA
58787 ATTTT-ATAA
1 ATTTTAATAA
58796 ATTTTAATAA
1 ATTTTAATAA
58806 TTATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTTAATAA
Found at i:64078 original size:58 final size:57
Alignment explanation
Indices: 63983--64101 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 57
63973 GGTAAGTAGC
* * * *
63983 AACAATTCCCAATGTCATGAATACTTTGACTAAGGTCATCTTCAGGCTAAGTGTGCG
1 AACAATTCCCAATGTAATGAATACCTTGACTAAGGTCATATTCAAGCTAAGTGTGCG
** *
64040 TAACAATTCCCAATGTAATGAATACCTTGGTTATGGTCATATTCAAGCTAAGTGTGCG
1 -AACAATTCCCAATGTAATGAATACCTTGACTAAGGTCATATTCAAGCTAAGTGTGCG
64098 AACA
1 AACA
64102 CTTTTAAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 4 0.07
58 50 0.93
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (57 bp):
AACAATTCCCAATGTAATGAATACCTTGACTAAGGTCATATTCAAGCTAAGTGTGCG
Found at i:66891 original size:3 final size:3
Alignment explanation
Indices: 66885--66920 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
66875 AAAGGATTTA
* *
66885 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT GAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
66921 ACCTTCCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:68525 original size:6 final size:6
Alignment explanation
Indices: 68510--68539 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
68500 CATGGGGGGG
68510 TTTTATT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTA-T TTTTAT TTTTAT TTTTAT TTTTA
68540 AGCAACTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:75385 original size:20 final size:20
Alignment explanation
Indices: 75347--75394 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
75337 ATATATATTA
75347 TCACTATTCACGACATGATC
1 TCACTATTCACGACATGATC
* * *
75367 TCACTGTTCATGACTTGAT-
1 TCACTATTCACGACATGATC
75386 TCCACTATT
1 T-CACTATT
75395 TCTAGGACTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (20 bp):
TCACTATTCACGACATGATC
Done.