Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014926.1 Kokia drynarioides strain JFW-HI SEQ_129969, 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: 60011
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 176 characters in sequence are not A, C, G, or T
Found at i:5288 original size:25 final size:23
Alignment explanation
Indices: 5247--5293 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
5237 CCAATTAGGG
5247 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
5270 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAG-ATTTAATTT
5294 GGATCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:5709 original size:15 final size:15
Alignment explanation
Indices: 5672--5710 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5662 TTATGTGTGC
*
5672 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
5687 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
5701 TTAATTCTTG
1 TTAATTCTTG
5711 TTTGATGCGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:6381 original size:21 final size:20
Alignment explanation
Indices: 6361--6403 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6351 AGCCATTTTA
6361 TTATTATTT--ATTTTTATT
1 TTATTATTTACATTTTTATT
*
6379 TTATTATTTACATTTTTAAT
1 TTATTATTTACATTTTTATT
6399 TTATT
1 TTATT
6404 TTTTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTATTTACATTTTTATT
Found at i:6412 original size:14 final size:15
Alignment explanation
Indices: 6391--6423 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6381 ATTATTTACA
6391 TTTT-TAATTT-ATT
1 TTTTCTAATTTAATT
6404 TTTTCTAATTTAATT
1 TTTTCTAATTTAATT
6419 TTTTC
1 TTTTC
6424 CCTTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 6 0.33
15 8 0.44
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTCTAATTTAATT
Found at i:11911 original size:12 final size:13
Alignment explanation
Indices: 11888--11912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11878 GTTTTTTTTT
11888 AATTGAAAAAAAA
1 AATTGAAAAAAAA
11901 AATTGAAAAAAA
1 AATTGAAAAAAA
11913 TTTGAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AATTGAAAAAAAA
Found at i:11965 original size:17 final size:17
Alignment explanation
Indices: 11943--11980 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
11933 AATTAGTATA
11943 TTTATTTTCAATTTTAT
1 TTTATTTTCAATTTTAT
*
11960 TTTATTTTTAATTTTAT
1 TTTATTTTCAATTTTAT
11977 TTTA
1 TTTA
11981 ATTATGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTCAATTTTAT
Found at i:12379 original size:27 final size:27
Alignment explanation
Indices: 12349--12445 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
12339 TTTTTATTAA
12349 TTTTATTTTGAGATTAATTTGTGACTC
1 TTTTATTTTGAGATTAATTTGTGACTC
* * * *
12376 TTTTATGTATTAGATGATTTAATGGAATTTTTATTAA
1 TTTTAT-T-TT-GA-GA-TTAAT----TTGTGACT-C
12413 TTTTATTTTGAGATTAATTTGTGACTC
1 TTTTATTTTGAGATTAATTTGTGACTC
12440 TTTTAT
1 TTTTAT
12446 GTATTAGATG
Statistics
Matches: 52, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
27 12 0.23
28 6 0.12
29 2 0.04
30 2 0.04
31 2 0.04
32 10 0.19
33 2 0.04
34 2 0.04
35 2 0.04
36 6 0.12
37 6 0.12
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (27 bp):
TTTTATTTTGAGATTAATTTGTGACTC
Found at i:12380 original size:36 final size:36
Alignment explanation
Indices: 12340--12445 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 36
12330 TATTTGGAAT
12340 TTTTATTAATTTTATTTTGAGATTAATTTGTGACTC
1 TTTTATTAATTTTATTTTGAGATTAATTTGTGACTC
** * *
12376 TTTTATGT-A--TTA-GATGA-TTTAA--TG-GAAT-
1 TTTTAT-TAATTTTATTTTGAGATTAATTTGTGACTC
12404 TTTTATTAATTTTATTTTGAGATTAATTTGTGACTC
1 TTTTATTAATTTTATTTTGAGATTAATTTGTGACTC
12440 TTTTAT
1 TTTTAT
12446 GTATTAGATG
Statistics
Matches: 52, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 3 0.06
30 5 0.10
31 3 0.06
32 8 0.15
33 3 0.06
34 5 0.10
35 3 0.06
36 13 0.25
37 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (36 bp):
TTTTATTAATTTTATTTTGAGATTAATTTGTGACTC
Found at i:12407 original size:64 final size:64
Alignment explanation
Indices: 12334--12462 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
12324 TTTTTCTATT
12334 TGGAATTTTTATTAATTTTATTTTGAGATTAATTTGTGACTCTTTTATGTATTAGATGATTTAA
1 TGGAATTTTTATTAATTTTATTTTGAGATTAATTTGTGACTCTTTTATGTATTAGATGATTTAA
12398 TGGAATTTTTATTAATTTTATTTTGAGATTAATTTGTGACTCTTTTATGTATTAGATGATTTAA
1 TGGAATTTTTATTAATTTTATTTTGAGATTAATTTGTGACTCTTTTATGTATTAGATGATTTAA
12462 T
1 T
12463 CTTTAAGATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (64 bp):
TGGAATTTTTATTAATTTTATTTTGAGATTAATTTGTGACTCTTTTATGTATTAGATGATTTAA
Found at i:14531 original size:15 final size:15
Alignment explanation
Indices: 14494--14532 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
14484 TTATGTGTGC
*
14494 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
14509 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
14523 TTAATTCTTG
1 TTAATTCTTG
14533 TTTGATGTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:15830 original size:12 final size:12
Alignment explanation
Indices: 15813--15889 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
15803 CCCAATAAAC
15813 TTAAAATTTATT
1 TTAAAATTTATT
*
15825 TTAAAATTGAGTTT
1 TTAAAATTTA--TT
*
15839 ATTATAAATTTA-A
1 -TTA-AAATTTATT
*
15852 TTAAAATTTATC
1 TTAAAATTTATT
* *
15864 AT-AAATTTAACT
1 TTAAAATTT-ATT
15876 TTAAAATTTATT
1 TTAAAATTTATT
15888 TT
1 TT
15890 TGTCCAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
11 13 0.27
12 19 0.39
13 6 0.12
14 2 0.04
15 3 0.06
16 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:15862 original size:22 final size:23
Alignment explanation
Indices: 15836--15887 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
15826 TAAAATTGAG
15836 TTTATTATAAATTTAA-TTAAAA
1 TTTATTATAAATTTAACTTAAAA
*
15858 TTTATCATAAATTTAACTTTAAAA
1 TTTATTATAAATTTAAC-TTAAAA
15882 TTTATT
1 TTTATT
15888 TTTGTCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 15 0.58
24 11 0.42
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATTATAAATTTAACTTAAAA
Found at i:16540 original size:12 final size:13
Alignment explanation
Indices: 16512--16544 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
16502 TGAGATTTAT
16512 TATTATTAAAGAA
1 TATTATTAAAGAA
16525 TATTATTAAA-AA
1 TATTATTAAAGAA
16537 TATTATTA
1 TATTATTA
16545 TTGGTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
TATTATTAAAGAA
Found at i:17669 original size:29 final size:29
Alignment explanation
Indices: 17626--17860 Score: 262
Period size: 29 Copynumber: 8.0 Consensus size: 29
17616 GGAGGTCCCT
* *
17626 AAACTATCCAAAAATCCCATTTTGACCTCG
1 AAACT-TCCAAAAATCCCATTTTTACCCCG
* * **
17656 AAACTTCCGAAAATCTCATTTTTAACCCAA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
17686 AAACTTCCAAAAATCCCATTTTTACCACCG
1 AAACTTCCAAAAATCCCATTTTTACC-CCG
*
17716 -AACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
* **
17745 AAACTTTCAAAAATTTCATTTTTACCCTCG
1 AAACTTCCAAAAATCCCATTTTTACCC-CG
*
17775 -AACTTCC-AAAATCCCATTTTTAACTCCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCG
*
17803 AAACTTCCAAAAATCTCATTTTTACCCCCG
1 AAACTTCCAAAAATCCCATTTTTA-CCCCG
17833 -AACTTCCAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATCCCATTTTT-ACCCC
17861 TAATTTTCCC
Statistics
Matches: 173, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
28 14 0.08
29 88 0.51
30 71 0.41
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:17875 original size:59 final size:59
Alignment explanation
Indices: 17626--17860 Score: 321
Period size: 59 Copynumber: 4.0 Consensus size: 59
17616 GGAGGTCCCT
* * * * * *
17626 AAACTATCCAAAAATCCCATTTTGA-CCTCGAAACTTCCGAAAATCTCATTTTTAACCCAA
1 AAACT-TCCAAAAATCTCATTTTTACCCCCG-AACTTCCAAAAATCCCATTTTTAACCCCA
* *
17686 AAACTTCCAAAAATCCCATTTTTACCACCGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * * *
17745 AAACTTTCAAAAATTTCATTTTTACCCTCGAACTTCC-AAAATCCCATTTTTAACTCCG
1 AAACTTCCAAAAATCTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
17803 AAACTTCCAAAAATCTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
17861 TAATTTTCCC
Statistics
Matches: 156, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
58 53 0.34
59 95 0.61
60 8 0.05
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (59 bp):
AAACTTCCAAAAATCTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:19046 original size:22 final size:22
Alignment explanation
Indices: 19018--19070 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
19008 CGCATATATT
19018 AATCTTATGCATTGTTCTTGCG
1 AATCTTATGCATTGTTCTTGCG
19040 AATCTTATGCATTGTTCTTGCG
1 AATCTTATGCATTGTTCTTGCG
19062 AATCTTATG
1 AATCTTATG
19071 TATAGTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (22 bp):
AATCTTATGCATTGTTCTTGCG
Found at i:22694 original size:84 final size:84
Alignment explanation
Indices: 22588--22752 Score: 303
Period size: 84 Copynumber: 2.0 Consensus size: 84
22578 AATTTTTAAA
*
22588 CTTATTTTTTGGACCGGATCGAATCTAAACCTAAAAAATGAACCTAAAATTTTATTGAGACTCGA
1 CTTATTTTTTGGACCGGATCGAATCTAAACCTAAAAAATGAACCTAAAATTTTATTGAGACCCGA
*
22653 TCTAATCCACAATCAAAGT
66 CCTAATCCACAATCAAAGT
22672 CTTATTTTTTGGACCGGATCGAATCTAAACCTAAAAAATGAACCTAAAATTTTATTGAGACCCGA
1 CTTATTTTTTGGACCGGATCGAATCTAAACCTAAAAAATGAACCTAAAATTTTATTGAGACCCGA
*
22737 CCTGATCCACAATCAA
66 CCTAATCCACAATCAA
22753 CGTTACATGA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (84 bp):
CTTATTTTTTGGACCGGATCGAATCTAAACCTAAAAAATGAACCTAAAATTTTATTGAGACCCGA
CCTAATCCACAATCAAAGT
Found at i:33912 original size:28 final size:28
Alignment explanation
Indices: 33872--33942 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
33862 TAACATTCAT
* *
33872 TAAACATAACATACGTAATATGCATAAA
1 TAAACATAACATACATAATATACATAAA
*
33900 TAAACATAACATACATAATATACATACA
1 TAAACATAACATACATAATATACATAAA
*
33928 TAAACAGTAAAATAC
1 TAAACA-TAACATAC
33943 TACATAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 31 0.82
29 7 0.18
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.24
Consensus pattern (28 bp):
TAAACATAACATACATAATATACATAAA
Found at i:34248 original size:30 final size:30
Alignment explanation
Indices: 34212--34285 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
34202 ACTAGAAGTC
*
34212 AGATATAATACAAATATAAAATTTGAACT-
1 AGATATAATACAAATACAAAATTTGAACTA
* ** *
34241 CGAATATAATATGAATACAAAATTTGAAGTA
1 AG-ATATAATACAAATACAAAATTTGAACTA
34272 AGATATAATACAAA
1 AGATATAATACAAA
34286 CAAAAACAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.28
Consensus pattern (30 bp):
AGATATAATACAAATACAAAATTTGAACTA
Found at i:35906 original size:25 final size:25
Alignment explanation
Indices: 35885--35931 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
35875 GAATAATCAC
35885 TAAACA-AATATAA-TTAATTAATA
1 TAAACACAATATAATTTAATTAATA
* *
35908 TAAATACTATATAATTTAATTAAT
1 TAAACACAATATAATTTAATTAAT
35932 TTTATTACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 6 0.30
25 9 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAACACAATATAATTTAATTAATA
Found at i:47495 original size:16 final size:16
Alignment explanation
Indices: 47474--47508 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
47464 CACTCAAAAT
47474 TACATCATCTTTTTTA
1 TACATCATCTTTTTTA
*
47490 TACATCATTTTTTTTA
1 TACATCATCTTTTTTA
47506 TAC
1 TAC
47509 TGATAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (16 bp):
TACATCATCTTTTTTA
Found at i:47709 original size:39 final size:39
Alignment explanation
Indices: 47666--47744 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
47656 ATTATAAAAC
*
47666 ACTTTGTTTCTATATCCACTTGATCTTCATGATCATAGA
1 ACTTTGTTTCCATATCCACTTGATCTTCATGATCATAGA
*
47705 ACTTTGTTTCCATATCCACTTGATTTTCATGATCATAGA
1 ACTTTGTTTCCATATCCACTTGATCTTCATGATCATAGA
47744 A
1 A
47745 GATTGGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (39 bp):
ACTTTGTTTCCATATCCACTTGATCTTCATGATCATAGA
Done.