Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013560.1 Kokia drynarioides strain JFW-HI SEQ_128586, 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: 47762
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3933 original size:18 final size:19
Alignment explanation
Indices: 3900--3942 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
3890 CATCAAATGG
*
3900 ATTAAATCGTAAAATATGA
1 ATTAAATCGGAAAATATGA
3919 ATTAAAT-GGAAAATATGA
1 ATTAAATCGGAAAATATGA
3937 A-TAAAT
1 ATTAAAT
3943 ACATTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (19 bp):
ATTAAATCGGAAAATATGA
Found at i:6450 original size:15 final size:15
Alignment explanation
Indices: 6430--6481 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
6420 GGATCCGTTA
*
6430 ACTCGACTCGATTTG
1 ACTCGAATCGATTTG
***
6445 ACTCGAATTTTTTTG
1 ACTCGAATCGATTTG
*
6460 ACTCGATTCGATTTG
1 ACTCGAATCGATTTG
*
6475 ATTCGAA
1 ACTCGAA
6482 AAATATTCAA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (15 bp):
ACTCGAATCGATTTG
Found at i:14251 original size:29 final size:31
Alignment explanation
Indices: 14218--14283 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
14208 TTTACGTTTT
*
14218 GGTCATCA-ACGTT-TCAATT-CTAACAATTA
1 GGTCAT-AGACGTTATCAATTAATAACAATTA
*
14247 GGTCATAGACGTTATCAATTAATAACAATTT
1 GGTCATAGACGTTATCAATTAATAACAATTA
14278 GGTCAT
1 GGTCAT
14284 TTCCCATTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 11 0.34
30 6 0.19
31 14 0.44
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (31 bp):
GGTCATAGACGTTATCAATTAATAACAATTA
Found at i:22252 original size:51 final size:51
Alignment explanation
Indices: 22193--22294 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
22183 ACATGGAAGT
* *
22193 CATGTCACCAATTAAC-GAGTCAGTTATGGTTTTTGTACAACACTATAAACA
1 CATGTCACCAATTAACAG-GTCAGTTATGATTTTCGTACAACACTATAAACA
*
22244 CATGTCACCATTTAACAGGTCAGTTATGATTTTCGTACAACACTATAAACA
1 CATGTCACCAATTAACAGGTCAGTTATGATTTTCGTACAACACTATAAACA
22295 AAAAATGATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (51 bp):
CATGTCACCAATTAACAGGTCAGTTATGATTTTCGTACAACACTATAAACA
Found at i:22910 original size:20 final size:19
Alignment explanation
Indices: 22871--22927 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
22861 TAAAAATAAA
* *
22871 TAATAATTTTCATAATTTTT
1 TAATAATTTTTAGAA-TTTT
22891 TAATATATTTTTAGAATTTT
1 TAATA-ATTTTTAGAATTTT
*
22911 TAATAATTTTTATAATT
1 TAATAATTTTTAGAATT
22928 ATTGTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.33
20 14 0.42
21 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATAATTTTTAGAATTTT
Found at i:22911 original size:9 final size:9
Alignment explanation
Indices: 22809--22927 Score: 60
Period size: 9 Copynumber: 12.8 Consensus size: 9
22799 TTGATTATTA
22809 TATAATTTT
1 TATAATTTT
*
22818 TAGAATTTT
1 TATAATTTT
* *
22827 TATGAGTTT
1 TATAATTTT
* *
22836 TCTATTTTT
1 TATAATTTT
**
22845 TAT-ATAAT
1 TATAATTTT
22853 TATAATTTT
1 TATAATTTT
* * **
22862 AAAAATAAAT
1 TATAAT-TTT
*
22872 AATAATTTT
1 TATAATTTT
*
22881 CATAATTTTT
1 TATAA-TTTT
22891 TAATATATTTT
1 T-ATA-ATTTT
*
22902 TAGAATTTT
1 TATAATTTT
22911 TAATAATTTT
1 T-ATAATTTT
22921 TATAATT
1 TATAATT
22928 ATTGTTAAAA
Statistics
Matches: 79, Mismatches: 25, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
8 5 0.06
9 45 0.57
10 20 0.25
11 8 0.10
12 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (9 bp):
TATAATTTT
Found at i:27732 original size:19 final size:19
Alignment explanation
Indices: 27703--27739 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
27693 TAAAAGTACC
27703 TAAACAATTAAAATATATTT
1 TAAACAATTAAAA-ATATTT
27723 TAAA-AATTAAAAATATT
1 TAAACAATTAAAAATATT
27740 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAACAATTAAAAATATTT
Found at i:27815 original size:24 final size:24
Alignment explanation
Indices: 27788--27837 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
27778 TTGAAACTCC
27788 TTAAAATTAAAAAAATA-AATAAAT
1 TTAAAATTAAAAAAATATAA-AAAT
*
27812 TTAAAATTATAAAAATATAAAAAT
1 TTAAAATTAAAAAAATATAAAAAT
27836 TT
1 TT
27838 TCATAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TTAAAATTAAAAAAATATAAAAAT
Found at i:30415 original size:55 final size:55
Alignment explanation
Indices: 30306--30470 Score: 165
Period size: 55 Copynumber: 3.0 Consensus size: 55
30296 ACGTACTATG
* * ** ** *
30306 TAACAATCAATTTAAATATATAAATAATTGATT-AATAAGAAGTAGCATTTCAACA
1 TAACAATCAATTTAAACATATAAATAATCGATTCAA-AAGAAACAATATTCCAACA
* *
30361 TAACAATCGATTTAAACATATAAATAATCAATTCAAAAGAAACAATATTCCAACA
1 TAACAATCAATTTAAACATATAAATAATCGATTCAAAAGAAACAATATTCCAACA
* * * *
30416 TAAGAATAAATTTAAGCATATGAAA-AAACGATTCAAAA-AAAGCAATATTCCAACA
1 TAACAATCAATTTAAACATAT-AAATAATCGATTCAAAAGAAA-CAATATTCCAACA
30471 ATTAAGAAGA
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
54 3 0.03
55 84 0.91
56 5 0.05
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.27
Consensus pattern (55 bp):
TAACAATCAATTTAAACATATAAATAATCGATTCAAAAGAAACAATATTCCAACA
Found at i:30729 original size:6 final size:6
Alignment explanation
Indices: 30720--30768 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
30710 GTAACATCCA
* * * *
30720 TTTCAT TTTCAT TTCCAT TTCCAT TTTCA- TATCAT TCTCAT TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
30767 TT
1 TT
30769 CATATTCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTCAT
Found at i:30732 original size:11 final size:11
Alignment explanation
Indices: 30718--30776 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
30708 CCGTAACATC
30718 CATTTCATTTT
1 CATTTCATTTT
*
30729 CATTTCCATTTC
1 CATTT-CATTTT
*
30741 CATTTTCA-TAT
1 CA-TTTCATTTT
30752 CATTCTCATTTT
1 CATT-TCATTTT
*
30764 CATTTCATATT
1 CATTTCATTTT
30775 CA
1 CA
30777 AATCATAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 2 0.05
11 19 0.49
12 15 0.38
13 3 0.08
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (11 bp):
CATTTCATTTT
Found at i:30738 original size:17 final size:17
Alignment explanation
Indices: 30716--30769 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
30706 AACCGTAACA
30716 TCCATTTCATTTTCATT
1 TCCATTTCATTTTCATT
*
30733 TCCATTTCCATTTTCATA
1 TCCATTT-CATTTTCATT
30751 T-CATTCTCATTTTCATT
1 TCCATT-TCATTTTCATT
30768 TC
1 TC
30770 ATATTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.56
Consensus pattern (17 bp):
TCCATTTCATTTTCATT
Found at i:30754 original size:23 final size:22
Alignment explanation
Indices: 30716--30773 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
30706 AACCGTAACA
*
30716 TCCATTTCATTTTCATT-TCCATT
1 TCCATTTCA-TATCATTCT-CATT
30739 TCCATTTTCATATCATTCTCATT
1 TCCA-TTTCATATCATTCTCATT
*
30762 TTCATTTCATAT
1 TCCATTTCATAT
30774 TCAAATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 8 0.26
23 17 0.55
24 6 0.19
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (22 bp):
TCCATTTCATATCATTCTCATT
Found at i:30771 original size:17 final size:16
Alignment explanation
Indices: 30718--30776 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 16
30708 CCGTAACATC
30718 CATTTCATTTTCATTT
1 CATTTCATTTTCATTT
*
30734 CCATTTCCATTTTCATAT
1 -CATTT-CATTTTCATTT
30752 CATTCTCATTTTCATTT
1 CATT-TCATTTTCATTT
30769 CATATTCA
1 CAT-TTCA
30777 AATCATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (16 bp):
CATTTCATTTTCATTT
Found at i:31583 original size:20 final size:20
Alignment explanation
Indices: 31560--31598 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31550 TATATATATA
31560 TATTACTTA-TAAAATATTAT
1 TATT-CTTAGTAAAATATTAT
*
31580 TATTTTTAGTAAAATATTA
1 TATTCTTAGTAAAATATTA
31599 AATAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TATTCTTAGTAAAATATTAT
Found at i:31696 original size:26 final size:26
Alignment explanation
Indices: 31667--31716 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
31657 TTTAGTTTCT
* *
31667 TCAAGAA-CATTTTATTTTTATTTTTA
1 TCAAGAATAATTTT-TTATTATTTTTA
31693 TCAAGAATAATTTTTTATTATTTT
1 TCAAGAATAATTTTTTATTATTTT
31717 AATACTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (26 bp):
TCAAGAATAATTTTTTATTATTTTTA
Found at i:37605 original size:17 final size:17
Alignment explanation
Indices: 37575--37608 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
37565 GAAGAAGTTC
* *
37575 AAAAATAAATACAAAAA
1 AAAAAAAAACACAAAAA
37592 AAAAAAAAACACAAAAA
1 AAAAAAAAACACAAAAA
37609 GCTATAGCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAAACACAAAAA
Found at i:42129 original size:30 final size:30
Alignment explanation
Indices: 42115--42256 Score: 141
Period size: 30 Copynumber: 4.8 Consensus size: 30
42105 AAAATTTCAT
42115 TTTTGACCCTTAAACTTTCTAAAAATTATG
1 TTTTGACCCTTAAACTTTCTAAAAATTATG
* *
42145 TTTTGGCCCTT-AACTTTCCAAAAATTAT-
1 TTTTGACCCTTAAACTTTCTAAAAATTATG
** *
42173 TTTT-AGCCCTCGAACTTTCTAAAAATTCA-A
1 TTTTGA-CCCTTAAACTTTCTAAAAATT-ATG
* * *
42203 ATTTGACCATCAAACTTTCTAAAAATTATG
1 TTTTGACCCTTAAACTTTCTAAAAATTATG
*
42233 TTTTGA-CCTCCAAACTTTCTAAAA
1 TTTTGACCCT-TAAACTTTCTAAAA
42257 TTTGAATTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
28 8 0.09
29 33 0.35
30 52 0.55
31 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTGACCCTTAAACTTTCTAAAAATTATG
Found at i:42265 original size:59 final size:59
Alignment explanation
Indices: 42156--42294 Score: 149
Period size: 59 Copynumber: 2.3 Consensus size: 59
42146 TTTGGCCCTT
* * *
42156 AACTTTCCAAAAATTATTTTTAGCCCTCGAACTTTCTAAAAATTCAAATTT-GACCATCA
1 AACTTTCAAAAAATTATTTTTAGACCTCAAACTTTCTAAAAATTCAAATTTAG-CCATCA
* ** *
42215 AACTTTCTAAAAATTATGTTTT-GACCTCCAAACTTTCT-AAAATTTGAATTTAGCCCTCA
1 AACTTTCAAAAAATTAT-TTTTAGACCT-CAAACTTTCTAAAAATTCAAATTTAGCCATCA
*
42274 AACTTTAAAAAAATTCATTTT
1 AACTTTCAAAAAATT-ATTTT
42295 GACCCCTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
59 52 0.76
60 16 0.24
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.38
Consensus pattern (59 bp):
AACTTTCAAAAAATTATTTTTAGACCTCAAACTTTCTAAAAATTCAAATTTAGCCATCA
Found at i:42275 original size:29 final size:30
Alignment explanation
Indices: 42121--42288 Score: 109
Period size: 30 Copynumber: 5.7 Consensus size: 30
42111 TCATTTTTGA
* * *
42121 CCCTTAAACTTTCTAAAAATTATG-TTTTGG
1 CCCTCAAACTTTCTAAAAATT-TGAATTTAG
* * *
42151 CCCT-TAACTTTCCAAAAA-TT-ATTTTTAG
1 CCCTCAAACTTTCTAAAAATTTGA-ATTTAG
* **
42179 CCCTCGAACTTTCTAAAAATTCAAATTT-G
1 CCCTCAAACTTTCTAAAAATTTGAATTTAG
* *
42208 ACCATCAAACTTTCTAAAAATTATG--TTTTG
1 -CCCTCAAACTTTCTAAAAATT-TGAATTTAG
*
42238 ACCTCCAAACTTTCT-AAAATTTGAATTTAG
1 CCCT-CAAACTTTCTAAAAATTTGAATTTAG
**
42268 CCCTCAAACTTTAAAAAAATT
1 CCCTCAAACTTTCTAAAAATT
42289 CATTTTGACC
Statistics
Matches: 109, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.01
28 12 0.11
29 44 0.40
30 51 0.47
31 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (30 bp):
CCCTCAAACTTTCTAAAAATTTGAATTTAG
Found at i:44342 original size:12 final size:12
Alignment explanation
Indices: 44325--44363 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
44315 TCAAAGAGAT
44325 ATGCAAGAACAA
1 ATGCAAGAACAA
**
44337 ATGCAAGCTCAA
1 ATGCAAGAACAA
*
44349 TTGCAAGAACAA
1 ATGCAAGAACAA
44361 ATG
1 ATG
44364 GCGAGAATGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (12 bp):
ATGCAAGAACAA
Found at i:47647 original size:21 final size:19
Alignment explanation
Indices: 47623--47678 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
47613 TTTTACCCAA
47623 AAAAAATAGAGAAAAGAAAAT
1 AAAAAA-AGA-AAAAGAAAAT
*
47644 AAAAGAAAAGAAAAAGGAAAT
1 -AAA-AAAAGAAAAAGAAAAT
47665 AGAAAAAAGAAAAA
1 A-AAAAAAGAAAAA
47679 AGGAGAGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 11 0.35
21 11 0.35
22 6 0.19
23 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAAT
Found at i:47679 original size:21 final size:21
Alignment explanation
Indices: 47622--47682 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
47612 CTTTTACCCA
* *
47622 AAAAAAATAGAGAAAAGAAAAT
1 AAAAAAA-AGAAAAAAGGAAAT
47644 AAAAGAAAAG-AAAAAGGAAAT
1 AAAA-AAAAGAAAAAAGGAAAT
*
47665 AGAAAAAAGAAAAAAGGA
1 AAAAAAAAGAAAAAAGGA
47683 GAGGTCAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 20 0.59
22 6 0.18
23 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAGGAAAT
Done.