Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009755.1 Kokia drynarioides strain JFW-HI SEQ_124474, 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: 40250
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2757 original size:20 final size:19
Alignment explanation
Indices: 2714--2757 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2704 ATATGATATT
2714 AATATTTTACTTTATTAAA
1 AATATTTTACTTTATTAAA
*
2733 AATATTTATATCTTT-TTATA
1 AATATTT-TA-CTTTATTAAA
2753 AATAT
1 AATAT
2758 AATGATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTTTACTTTATTAAA
Found at i:4412 original size:64 final size:63
Alignment explanation
Indices: 4321--4478 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 63
4311 TTATTTATTT
4321 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTA-TTTTAC
* *
4385 ATTTATTTATTTATATTCATACAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAT
1 ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
4448 ATTTATTTATTTATATTCATAAAAATAATAA
1 ATTTATTTATTTATATTCAT-AAAATAATAA
4479 GAAAAATGAA
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 25 0.28
64 65 0.72
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (63 bp):
ATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
Found at i:5115 original size:39 final size:39
Alignment explanation
Indices: 5000--5358 Score: 310
Period size: 39 Copynumber: 9.3 Consensus size: 39
4990 ATAGCTTCAG
* *
5000 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGG-TC
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA
* * *
5038 GAG-ATCAA-A-T-GA-T-CTTCAATCTGCCTTC-TGGTTA
1 GGGTA-AAAGATTGGATTGCTTCAATCTGCC-CCATGGTTA
* **
5072 GGGTAAAAGATTGGATTGCTTCAATTTGCCCCATGGTCG
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA
* * * * **
5111 GGGTAAGAGATCGGATGGTCTTCAATTTGCCCTTTGGTTA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTTA
* * *
5151 GGGTAAACGATTGGATTGCTTCAATCTGCCCCAT-TTTCG
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT-A
* * * * *
5190 GGGTAAGAGATCGGATGGTCTTCAATCTGCGCTC-TAGTTA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGC-CCCATGGTTA
5230 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTT-
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA
* * * *
5268 GGGATAAGAGATCGGATGGTCTTCAATCTGCCCTC-TAGTTA
1 GGG-TAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTTA
*
5309 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTTA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA
5348 GGGTAAAAGAT
1 GGGTAAAAGAT
5359 CAGATGGTCC
Statistics
Matches: 252, Mismatches: 48, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
33 14 0.06
34 7 0.03
35 4 0.02
36 2 0.01
37 4 0.02
38 14 0.06
39 112 0.44
40 87 0.35
41 8 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (39 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTA
Found at i:5169 original size:79 final size:79
Alignment explanation
Indices: 5050--5420 Score: 519
Period size: 79 Copynumber: 4.7 Consensus size: 79
5040 GATCAAATGA
* * *
5050 TCTTCAATCTGCCTTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCCCATGGTCGGGGT
1 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGT
5115 AAGAGATCGGATGG
66 AAGAGATCGGATGG
* * * * **
5129 TCTTCAATTTGCCCTTTGGTTAGGGTAAACGATTGGATTGCTTCAATCTGCCCCATTTTCGGGGT
1 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGT
5194 AAGAGATCGGATGG
66 AAGAGATCGGATGG
* * *
5208 TCTTCAATCTGCGCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTGGGAT
1 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGT
5273 AAGAGATCGGATGG
66 AAGAGATCGGATGG
* **
5287 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTTAGGGT
1 TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGT
* *
5352 AAAAGATCAGATGG
66 AAGAGATCGGATGG
** * *
5366 TCCTT-AATCTGTTCTCTAGTTAGGGTAAAAGATTCGAATGGTCTTCAATCTGCCC
1 T-CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATT-GGATTG-CTTCAATCTGCCC
5421 ATTTCAGCTT
Statistics
Matches: 262, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
79 243 0.93
80 7 0.03
81 12 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (79 bp):
TCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGT
AAGAGATCGGATGG
Found at i:5281 original size:158 final size:157
Alignment explanation
Indices: 5000--5420 Score: 527
Period size: 158 Copynumber: 2.7 Consensus size: 157
4990 ATAGCTTCAG
* * * * *
5000 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGG-T--CG----AGATCAAATGATCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTTAGGGTAAAAGATCAGATGGTCTTCAAT
* * *
5058 CTGCCTTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCCCATGGTCGGGGTAAGAGATC
66 CTGCC-TCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGATAAGAGATC
* * *
5123 GGATGGTCTTCAATTTGCCCTTTGGTTA
130 GGATGGTCTTCAATCTGCCCTCTAGTTA
* * * * * *
5151 GGGTAAACGATTGGATTGCTTCAATCTGCCCCAT-TTTCGGGGTAAGAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTT-AGGGTAAAAGATCAGATGGTCTTCAA
*
5215 TCTGCGCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTGGGATAAGAGAT
65 TCTGC-CTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGATAAGAGAT
5280 CGGATGGTCTTCAATCTGCCCTCTAGTTA
129 CGGATGGTCTTCAATCTGCCCTCTAGTTA
5309 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTTAGGGTAAAAGATCAGATGGTCCTT-AA
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTTAGGGTAAAAGATCAGATGGT-CTTCAA
* * *
5373 TCTGTTCTCTAGTTAGGGTAAAAGATTCGAATGGTCTTCAATCTGCCC
65 TCTG-CCTCTAGTTAGGGTAAAAGATT-GGATTG-CTTCAATCTGCCC
5421 ATTTCAGCTT
Statistics
Matches: 233, Mismatches: 23, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
151 33 0.14
154 1 0.00
158 176 0.76
159 10 0.04
160 13 0.06
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (157 bp):
GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTTAGGGTAAAAGATCAGATGGTCTTCAAT
CTGCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGATAAGAGATCG
GATGGTCTTCAATCTGCCCTCTAGTTA
Found at i:5532 original size:50 final size:50
Alignment explanation
Indices: 5438--5532 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
5428 CTTCAGGAGT
*
5438 ATAAGATTCGTCCTTGCGACTTCAATCTGCTCCTCTACAGCTTTAAATGA
1 ATAAGATTCGTCCTTGCGACTTCAATCTGCTCCTCTACAACTTTAAATGA
* *
5488 ATAAGATTCG-CCATTGCGACTTCAATCT-ATCCCTTTACAACTTTA
1 ATAAGATTCGTCC-TTGCGACTTCAATCTGCT-CCTCTACAACTTTA
5533 GGTATATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (50 bp):
ATAAGATTCGTCCTTGCGACTTCAATCTGCTCCTCTACAACTTTAAATGA
Found at i:6531 original size:38 final size:38
Alignment explanation
Indices: 6475--6557 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
6465 CCCATCTTTT
* *
6475 TTTTTATTTGAGCGGCCCTTTACGGGTTTTCAACTCAAC
1 TTTTT-TTTGAGCCGCCCTTTACGGGTTTTCAACACAAC
**
6514 TTTTTTTTGAGCCGCCCTTTGTGGGTTTTCAACACAAC
1 TTTTTTTTGAGCCGCCCTTTACGGGTTTTCAACACAAC
6552 TTTTTT
1 TTTTTT
6558 CTTTTTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 35 0.88
39 5 0.12
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.46
Consensus pattern (38 bp):
TTTTTTTTGAGCCGCCCTTTACGGGTTTTCAACACAAC
Found at i:10413 original size:31 final size:31
Alignment explanation
Indices: 10362--10441 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
10352 CGTCTTTCTC
10362 AAACTTT-T-AATGCATGAAAATACGATGCA
1 AAACTTTATGAATGCATGAAAATACGATGCA
* * *
10391 AAACTTTATGAATGCATTAAAATGCGATGCG
1 AAACTTTATGAATGCATGAAAATACGATGCA
*
10422 AAATTTTATGAATGCATGAA
1 AAACTTTATGAATGCATGAA
10442 TGCATATGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 7 0.16
30 1 0.02
31 36 0.82
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (31 bp):
AAACTTTATGAATGCATGAAAATACGATGCA
Found at i:13025 original size:67 final size:67
Alignment explanation
Indices: 12912--13090 Score: 242
Period size: 67 Copynumber: 2.7 Consensus size: 67
12902 TTCGGGTTTG
* * *
12912 TTATTTATTTATTTATCTATATTCATAAAATAATAAAT-AAT--A-AATAAAGCAAAATTAATAT
1 TTATTCATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAACAAAATTAATAT
12973 TA
66 TA
*
12975 TT-TTACATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAATTAATA
1 TTATT-CATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAACAAAATTAATA
13039 TTA
65 TTA
* * *
13042 TTATTTATTTGTTTATTTATATTCAAAATAATAATAAATAAATAAATAA
1 TTATTCATTTATTTATTTATATTCATAA-AATAATAAATAAATAAATAA
13091 AATAAATAAG
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
62 2 0.02
63 32 0.32
64 3 0.03
66 1 0.01
67 41 0.41
68 22 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (67 bp):
TTATTCATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAACAAAATTAATAT
TA
Found at i:13105 original size:17 final size:17
Alignment explanation
Indices: 13066--13105 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
13056 ATTTATATTC
13066 AAAATAATAATAAATAA
1 AAAATAATAATAAATAA
13083 ATAAATAA-AATAAATAA
1 A-AAATAATAATAAATAA
13100 GAAAAT
1 -AAAAT
13106 TGGAATTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAATAATAATAAATAA
Found at i:13520 original size:18 final size:19
Alignment explanation
Indices: 13496--13550 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 19
13486 AACTGACCTC
13496 CAACCGAATTAAATCGATT
1 CAACCGAATTAAATCGATT
*
13515 -AACCGAATTAAATCAATT
1 CAACCGAATTAAATCGATT
* *
13533 CAATCG-ATTAATTCGATT
1 CAACCGAATTAAATCGATT
13551 TTAACCGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (19 bp):
CAACCGAATTAAATCGATT
Found at i:17683 original size:8 final size:9
Alignment explanation
Indices: 17667--17691 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17657 TTGATTTTAT
17667 ATAAAAAAA
1 ATAAAAAAA
17676 ATAAAAAAA
1 ATAAAAAAA
17685 ATAAAAA
1 ATAAAAA
17692 TATCATCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:19479 original size:28 final size:28
Alignment explanation
Indices: 19448--19501 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
19438 TCAACGCTTG
* *
19448 GAACATGATGTTGGTTAC-TTATTATTTC
1 GAACAT-ATATTGATTACTTTATTATTTC
*
19476 GAACCTATATTGATTACTTTATTATT
1 GAACATATATTGATTACTTTATTATT
19502 GGTTAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (28 bp):
GAACATATATTGATTACTTTATTATTTC
Found at i:22691 original size:36 final size:36
Alignment explanation
Indices: 22650--22738 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
22640 CATATAGTAG
* * *
22650 CATGTTTTACATGTGAATCAGATTAACAGAAAATAA
1 CATGTTTAACATGCGAATCAGATTAACAAAAAATAA
22686 CATGTTTAACATGCGAATCAGATTAACAAAAAATAA
1 CATGTTTAACATGCGAATCAGATTAACAAAAAATAA
22722 CATGTTTAACATGCGAA
1 CATGTTTAACATGCGAA
22739 CTCGTATATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (36 bp):
CATGTTTAACATGCGAATCAGATTAACAAAAAATAA
Found at i:22696 original size:19 final size:19
Alignment explanation
Indices: 22672--22732 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
22662 GTGAATCAGA
22672 TTAACAGAAAATAACATGT
1 TTAACAGAAAATAACATGT
** *
22691 TTAACATGCGAAT--CA-GA
1 TTAACA-GAAAATAACATGT
*
22708 TTAACAAAAAATAACATGT
1 TTAACAGAAAATAACATGT
22727 TTAACA
1 TTAACA
22733 TGCGAACTCG
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 4 0.13
19 13 0.42
20 4 0.13
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (19 bp):
TTAACAGAAAATAACATGT
Found at i:32065 original size:21 final size:21
Alignment explanation
Indices: 32039--32090 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
32029 TGAGACAATA
32039 CTACCGATACAAGTATAACTT
1 CTACCGATACAAGTATAACTT
* * * **
32060 CTACCGAAACATGTTTTGCTT
1 CTACCGATACAAGTATAACTT
32081 CTACCGATAC
1 CTACCGATAC
32091 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
CTACCGATACAAGTATAACTT
Found at i:37953 original size:7 final size:7
Alignment explanation
Indices: 37938--37967 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
37928 TCAAACATTT
*
37938 TTTTTTC
1 TTTTCTC
37945 TTTTCTC
1 TTTTCTC
37952 TTTTCTC
1 TTTTCTC
37959 TTTTCTC
1 TTTTCTC
37966 TT
1 TT
37968 CTCTTTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTCTC
Found at i:38605 original size:17 final size:17
Alignment explanation
Indices: 38551--38605 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
38541 TATATATGGA
*
38551 AATGCAATGACAAT-GT
1 AATGCAATGACAATAAT
* *
38567 ACATGCAACGACAATAAA
1 A-ATGCAATGACAATAAT
*
38585 AATGCAATGACATTAAT
1 AATGCAATGACAATAAT
38602 AATG
1 AATG
38606 TAGGAACAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (17 bp):
AATGCAATGACAATAAT
Done.