Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005225.1 Kokia drynarioides strain JFW-HI SEQ_119108, 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: 34163
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:335 original size:150 final size:149
Alignment explanation
Indices: 2--521 Score: 733
Period size: 150 Copynumber: 3.4 Consensus size: 149
1 A
*
2 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * *
67 GTTAAAAGTTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTATTTTTTTTTTAAAAATC
66 GTAAAAAATTT--ACTTTTTCTTTAAAATAACTAAAAAACAGA-TTT-TTATTTTTTT-AAAATC
132 TAAACTTTCTTTTTTTTTT-AAAG
126 TAAACTTTCTTTTTTTTTTAAAAG
*
155 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTA-AAAAAATCAAAACTT
* * * *
220 TGTCAAAAATTTTCTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTTTAAACTCTAAA
65 TGTAAAAAATTTACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCTAAA
285 CTTTCTTTTTTTTTTAAAAG
130 CTTTCTTTTTTTTTTAAAAG
*
305 AAAATCACTATTTTGCTTAAAAATCCAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTA-AAAAAATCAAAACTT
* * *
370 TGTTAAAAAATTAAAATTTTTCTTTAAAATAACT-AAAAACAGATTTTTATTTTTTAAAAATCTA
65 TG-TAAAAAATT-TACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCTA
*
434 AATTTTCTGTTTTTTTTTTTAAAAG
128 AACTTTC---TTTTTTTTTTAAAAG
* *
459 AAAATCACTATTTTGCTTAAAAAAT-CAAAGCTTTTATTTCGAAATTGTTTAAAAAAA-CAAAAC
1 AAAATCACTATTTTACTT-AAAAATCCAAA-CTTTTATTTCGAAATAG-TTAAAAAAATCAAAAC
522 ATTTCCCAAA
Statistics
Matches: 338, Mismatches: 19, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
149 24 0.07
150 78 0.23
151 44 0.13
152 46 0.14
153 47 0.14
154 68 0.20
155 28 0.08
156 3 0.01
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (149 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTAAAAAATTTACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTTAAAATCTAAAC
TTTCTTTTTTTTTTAAAAG
Found at i:1028 original size:11 final size:11
Alignment explanation
Indices: 1014--1038 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1004 TCCAAAATGG
1014 AAAGAAAAATA
1 AAAGAAAAATA
1025 AAAGAAAAATA
1 AAAGAAAAATA
1036 AAA
1 AAA
1039 ACCTCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:4043 original size:19 final size:20
Alignment explanation
Indices: 4008--4045 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3998 GTTTCCTGGA
4008 AAAAGTCAACTGGTCAACAG
1 AAAAGTCAACTGGTCAACAG
4028 AAAAGTCAAC-GGTCAACA
1 AAAAGTCAACTGGTCAACA
4046 ATTTAGTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (20 bp):
AAAAGTCAACTGGTCAACAG
Found at i:5444 original size:56 final size:56
Alignment explanation
Indices: 5366--5472 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
5356 GAAATCAAAA
* *
5366 TTCTTTTTGCATTATTCAATTGATCACTTTTGATAAAGAACGATCTGCAATCAGAT
1 TTCTTTTTACATTATTCAATTGATCACTTTTGATAAAGAACGAACTGCAATCAGAT
* *
5422 TTCTTTTTATATTATTTAATTGATCACTTTTGATAAAGAACGAACTGCAAT
1 TTCTTTTTACATTATTCAATTGATCACTTTTGATAAAGAACGAACTGCAAT
5473 GAACACTACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (56 bp):
TTCTTTTTACATTATTCAATTGATCACTTTTGATAAAGAACGAACTGCAATCAGAT
Found at i:5486 original size:56 final size:56
Alignment explanation
Indices: 5376--5485 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 56
5366 TTCTTTTTGC
* * * * *
5376 ATTATTCAATTGATCACTTTTGATAAAGAACGATCTGCAATCAGATTTCTTTTTAT
1 ATTATTCAATTGATCACTTTTGATAAAGAACGAACTGCAATAACACTACTTTTTAT
*
5432 ATTATTTAATTGATCACTTTTGATAAAGAACGAACTGCAATGAACACTACTTTT
1 ATTATTCAATTGATCACTTTTGATAAAGAACGAACTGCAAT-AACACTACTTTT
5486 AATAATACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 39 0.83
57 8 0.17
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (56 bp):
ATTATTCAATTGATCACTTTTGATAAAGAACGAACTGCAATAACACTACTTTTTAT
Found at i:6752 original size:29 final size:29
Alignment explanation
Indices: 6704--6779 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
6694 ATTGGTACAT
* * *
6704 AGTACCTGATAAATATAACA-TAGGCACAA
1 AGTACTTGATAACTGTAACACT-GGCACAA
* *
6733 AGTGCTTGATAACTGTAACACTGGTACAA
1 AGTACTTGATAACTGTAACACTGGCACAA
6762 AGTACTTGATAACTGTAA
1 AGTACTTGATAACTGTAA
6780 TCACCGACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (29 bp):
AGTACTTGATAACTGTAACACTGGCACAA
Found at i:10950 original size:16 final size:15
Alignment explanation
Indices: 10931--10982 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 15
10921 CTTAAGACCA
10931 AAAAAATTTAAACTC
1 AAAAAATTTAAACTC
* *
10946 GAAAAAACTTAAATTC
1 -AAAAAATTTAAACTC
*
10962 AAAAAATCTAAA-TC
1 AAAAAATTTAAACTC
*
10976 TAAAAAT
1 AAAAAAT
10983 AATCTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 8 0.26
15 10 0.32
16 13 0.42
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAAAATTTAAACTC
Found at i:19851 original size:21 final size:22
Alignment explanation
Indices: 19825--19870 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
19815 TAAAAGTTAT
*
19825 AAAATA-TTAAATTTTAATAAA
1 AAAATATTTAAAATTTAATAAA
*
19846 AAAATATTTAAAATTTATTAAA
1 AAAATATTTAAAATTTAATAAA
19868 AAA
1 AAA
19871 TAGAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATATTTAAAATTTAATAAA
Found at i:19877 original size:9 final size:9
Alignment explanation
Indices: 19865--19898 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19855 AAAATTTATT
19865 AAAAAATAG
1 AAAAAATAG
*
19874 AAAATATAG
1 AAAAAATAG
19883 AAAAAAATAG
1 -AAAAAATAG
19893 AAAAAA
1 AAAAAA
19899 AATTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAAAAATAG
Found at i:19918 original size:19 final size:20
Alignment explanation
Indices: 19896--19970 Score: 52
Period size: 19 Copynumber: 3.9 Consensus size: 20
19886 AAAATAGAAA
* *
19896 AAAAATTAT-AAAATTTTAT
1 AAAAATCATAAAAATATTAT
19915 -AAAATCATAAAAATATTAT
1 AAAAATCATAAAAATATTAT
*
19934 AGAAAAT-GTAAATAA-A-TAT
1 A-AAAATCATAAA-AATATTAT
*
19953 AAAATTCATGAAAAATAT
1 AAAAATCAT-AAAAATAT
19971 AAAAATTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
18 11 0.26
19 16 0.37
20 9 0.21
21 7 0.16
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAAATCATAAAAATATTAT
Found at i:20080 original size:13 final size:14
Alignment explanation
Indices: 20057--20085 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20047 TTTGGATGCA
20057 TTTTATAGTTTTTT
1 TTTTATAGTTTTTT
20071 TTTTAT-GTTTTTT
1 TTTTATAGTTTTTT
20084 TT
1 TT
20086 ATAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (14 bp):
TTTTATAGTTTTTT
Found at i:21790 original size:15 final size:15
Alignment explanation
Indices: 21770--21798 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21760 GGAAGGACTG
21770 GGTGGTGCTGGAGGT
1 GGTGGTGCTGGAGGT
21785 GGTGGTGCTGGAGG
1 GGTGGTGCTGGAGG
21799 AGAAAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.62, T:0.24
Consensus pattern (15 bp):
GGTGGTGCTGGAGGT
Found at i:24989 original size:27 final size:30
Alignment explanation
Indices: 24959--25023 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 30
24949 TTTAATTTTT
24959 ATTTAGGGTTATTTA-A-ATAT-TAGTTTG
1 ATTTAGGGTTATTTACATATATATAGTTTG
* *
24986 ATTTA---TTATTTACATATTTATATTTTG
1 ATTTAGGGTTATTTACATATATATAGTTTG
25013 ATTTAGGGTTA
1 ATTTAGGGTTA
25024 GTATTCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
24 7 0.23
25 1 0.03
26 3 0.10
27 16 0.53
30 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTAGGGTTATTTACATATATATAGTTTG
Found at i:25414 original size:30 final size:32
Alignment explanation
Indices: 25354--25423 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
25344 TTGCATGTGT
* *
25354 TGTATTAAATGTTTGTTTATAGTCTGATAGTGA
1 TGTAGTAAATGCTTGTTTATA-TCTGATAGTGA
*
25387 TGTAGTAAATGCTTGTTTAT-T-TGATAGTTA
1 TGTAGTAAATGCTTGTTTATATCTGATAGTGA
25417 TG-AGTAA
1 TGTAGTAA
25424 TTTGTTTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.15
30 10 0.29
31 1 0.03
33 18 0.53
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (32 bp):
TGTAGTAAATGCTTGTTTATATCTGATAGTGA
Found at i:27215 original size:24 final size:22
Alignment explanation
Indices: 27188--27255 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 22
27178 CTATTTTGAC
27188 TTGTATGCTTTTTTTAATATTATT
1 TTGTATG-TTTTTTTAATA-TATT
* *
27212 TTGTATGTTATTCTTTATTATGTT
1 TTGTATGTT-TT-TTTAATATATT
27236 TTGTATGTTGTTTTTTAATA
1 TTGTATG-T-TTTTTTAATA
27256 CCTTAAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 25 0.68
25 9 0.24
26 1 0.03
ACGTcount: A:0.19, C:0.03, G:0.12, T:0.66
Consensus pattern (22 bp):
TTGTATGTTTTTTTAATATATT
Found at i:27338 original size:12 final size:11
Alignment explanation
Indices: 27289--27343 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
27279 TGCTGTGTTT
*
27289 TGTTGGCTTTA
1 TGTTGACTTTA
*
27300 TGATGACTTTA
1 TGTTGACTTTA
27311 TGTCT-ACTTTA
1 TGT-TGACTTTA
*
27322 TGTTGGCTTTAA
1 TGTTGACTTT-A
27334 TGTTGACTTT
1 TGTTGACTTT
27344 CTATTGGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 1 0.03
11 24 0.67
12 11 0.31
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (11 bp):
TGTTGACTTTA
Found at i:28057 original size:21 final size:21
Alignment explanation
Indices: 28033--28091 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
28023 ACCCCAACTT
28033 AGCAAGTGAGCAACACATCTC
1 AGCAAGTGAGCAACACATCTC
* * *
28054 AGCAATTGAGTAATACATCTC
1 AGCAAGTGAGCAACACATCTC
*
28075 AGCAAGGGAGCAACACA
1 AGCAAGTGAGCAACACA
28092 ACTCCATTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (21 bp):
AGCAAGTGAGCAACACATCTC
Found at i:29004 original size:16 final size:16
Alignment explanation
Indices: 28973--29007 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28963 AAACCAGCTG
**
28973 CCATGAGAAGTGACAA
1 CCATGAGAAGCAACAA
28989 CCATGAGAAGCAACAA
1 CCATGAGAAGCAACAA
29005 CCA
1 CCA
29008 ACAAAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.26, G:0.20, T:0.09
Consensus pattern (16 bp):
CCATGAGAAGCAACAA
Found at i:29335 original size:3 final size:3
Alignment explanation
Indices: 29327--29428 Score: 154
Period size: 3 Copynumber: 34.7 Consensus size: 3
29317 ATGGCCGAAA
* * * *
29327 TCT TCT TCT TCT TCT TCT TCT TC- TCT T-T TTT TAT TCT CCT TCT TAT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
29373 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
29421 TCT TCT TC
1 TCT TCT TC
29429 CTCCTCCTCC
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
2 4 0.04
3 87 0.96
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:33412 original size:20 final size:19
Alignment explanation
Indices: 33387--33439 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
33377 AAATTAAATC
***
33387 TAATATTAAAATAATCACTT
1 TAATATTAAAATAAT-AAAA
*
33407 TAATATTAAATTAATAAAA
1 TAATATTAAAATAATAAAA
33426 TAATATTAAAATAA
1 TAATATTAAAATAA
33440 GTATTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATATTAAAATAATAAAA
Found at i:33420 original size:11 final size:11
Alignment explanation
Indices: 33406--33481 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
33396 AATAATCACT
33406 TTAATATTAAA
1 TTAATATTAAA
33417 TTAATA--AAA
1 TTAATATTAAA
33426 -TAATATTAAA
1 TTAATATTAAA
*
33436 ATAAGTATTAAA
1 TTAA-TATTAAA
33448 TTACAT-TTAATA
1 TTA-ATATTAA-A
33460 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
33473 ATAATATTA
1 TTAATATTA
33482 TTTTTGGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
8 5 0.09
9 3 0.06
10 3 0.06
11 18 0.33
12 16 0.30
13 5 0.09
14 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Done.