Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010922.1 Kokia drynarioides strain JFW-HI SEQ_125890, 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: 18685
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:2518 original size:47 final size:47
Alignment explanation
Indices: 2449--2543 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
2439 TTACAAAATG
2449 ATAGAAGATTGGCATGACAAATTCATTGGTAATCGCTGGAATGTCCA
1 ATAGAAGATTGGCATGACAAATTCATTGGTAATCGCTGGAATGTCCA
2496 ATAGAAGATTGGCATGACAAATTCATTGGTAATCGCTGGAATGTCCA
1 ATAGAAGATTGGCATGACAAATTCATTGGTAATCGCTGGAATGTCCA
2543 A
1 A
2544 GGATAACTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (47 bp):
ATAGAAGATTGGCATGACAAATTCATTGGTAATCGCTGGAATGTCCA
Found at i:3175 original size:14 final size:14
Alignment explanation
Indices: 3156--3183 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3146 TTTTTCTATC
3156 TTGTTACCAAAAAT
1 TTGTTACCAAAAAT
3170 TTGTTACCAAAAAT
1 TTGTTACCAAAAAT
3184 AAAAAAACAT
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TTGTTACCAAAAAT
Found at i:7566 original size:17 final size:18
Alignment explanation
Indices: 7534--7592 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
7524 ATTTTTTTTT
*
7534 AATTTTTTATAGTTTTTAC
1 AATTTTTTA-AATTTTTAC
7553 TAA-TTTTT-AATTTTTAC
1 -AATTTTTTAAATTTTTAC
*
7570 AATTTTTTAAATTTTTAA
1 AATTTTTTAAATTTTTAC
7588 AATTT
1 AATTT
7593 AAACATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 2 0.06
17 13 0.37
18 13 0.37
19 5 0.14
20 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (18 bp):
AATTTTTTAAATTTTTAC
Found at i:7576 original size:27 final size:25
Alignment explanation
Indices: 7529--7587 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
7519 AAAATATTTT
*
7529 TTTTTAATTTTTTATAGTTTTTACTAA
1 TTTTTAATTTTTTAAAGTTTTTA--AA
*
7556 TTTTTAA-TTTTTACAATTTTTTAAA
1 TTTTTAATTTTTTA-AAGTTTTTAAA
7581 TTTTTAA
1 TTTTTAA
7588 AATTTAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.31
26 6 0.21
27 14 0.48
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTTAATTTTTTAAAGTTTTTAAA
Found at i:7577 original size:18 final size:18
Alignment explanation
Indices: 7534--7592 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
7524 ATTTTTTTTT
*
7534 AATTTTTTATAGTTTTTAC
1 AATTTTTT-TAATTTTTAC
7553 TAA--TTTTTAATTTTTAC
1 -AATTTTTTTAATTTTTAC
* *
7570 AATTTTTTAAATTTTTAA
1 AATTTTTTTAATTTTTAC
7588 AATTT
1 AATTT
7593 AAACATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 9 0.26
18 21 0.62
20 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (18 bp):
AATTTTTTTAATTTTTAC
Found at i:7588 original size:8 final size:8
Alignment explanation
Indices: 7529--7588 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
7519 AAAATATTTT
*
7529 TTTTTAAT
1 TTTTTAAA
*
7537 TTTTTATAG
1 TTTTTA-AA
7546 TTTTTACTAA
1 TTTTTA--AA
7556 TTTTT-AA
1 TTTTTAAA
7563 TTTTTACAA
1 TTTTTA-AA
7572 TTTTTTAAA
1 -TTTTTAAA
7581 TTTTTAAA
1 TTTTTAAA
7589 ATTTAAACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
7 7 0.16
8 14 0.31
9 11 0.24
10 13 0.29
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTTTAAA
Found at i:7607 original size:25 final size:24
Alignment explanation
Indices: 7548--7607 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
7538 TTTTATAGTT
* ** *
7548 TTTACTAATTTTTAATTTTTACAA
1 TTTATTAATTTTTAAAATTTAAAA
*
7572 TTTTTTAAATTTTTAAAATTTAAACA
1 TTTATT-AATTTTTAAAATTTAAA-A
7598 TTTATTAATT
1 TTTATTAATT
7608 GTTGACGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.14
25 18 0.64
26 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTATTAATTTTTAAAATTTAAAA
Found at i:8408 original size:24 final size:23
Alignment explanation
Indices: 8337--8416 Score: 78
Period size: 24 Copynumber: 3.6 Consensus size: 23
8327 AGAAGTTAAG
8337 ATAATTATATATTTAAAAATAATT
1 ATAATTA-ATATTTAAAAATAATT
* ** *
8361 ATAATT--TA-TTAAAAGTTGTG
1 ATAATTAATATTTAAAAATAATT
8381 ATAATTACATATTTAAAAATAATT
1 ATAATTA-ATATTTAAAAATAATT
8405 ATAATTAA-ATTT
1 ATAATTAATATTT
8417 TTAATTATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 14 0.32
21 2 0.05
22 4 0.09
23 3 0.07
24 21 0.48
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (23 bp):
ATAATTAATATTTAAAAATAATT
Found at i:9650 original size:39 final size:39
Alignment explanation
Indices: 9585--9678 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
9575 CATGGCTTGG
* *
9585 ACACACGCTAGTGCATCAGCCCGTGTGCCTTACACAGTCTA
1 ACACACGCTCGTG--TCAGCCCGTGTGCCTCACACAGTCTA
* * **
9626 ACACACGCTCGTGTCAGCCTGTGTGCGTCACATGGTCTA
1 ACACACGCTCGTGTCAGCCCGTGTGCCTCACACAGTCTA
* *
9665 ACACAAGCCCGTGT
1 ACACACGCTCGTGT
9679 TATCTGCCCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
39 33 0.73
41 12 0.27
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (39 bp):
ACACACGCTCGTGTCAGCCCGTGTGCCTCACACAGTCTA
Found at i:12603 original size:96 final size:96
Alignment explanation
Indices: 12419--12610 Score: 228
Period size: 96 Copynumber: 2.0 Consensus size: 96
12409 TTTTTGTGAA
** * *
12419 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCCAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCCAGTAAGTTAAGACACAATATTTCA
* *
12484 AAATCTAAGATAATGAAACATTGCCTCGATT
66 AAATCGAAGATAAAGAAACATTGCCTCGATT
* * * * *
12515 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGACACAA-ATTTTA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCCAGTAAGTTAAGACACAATATTTCA
*
12579 GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
66 -AAA-TCGAAGATAAAGA-AACATTGCCTCGATT
12611 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
95 6 0.07
96 71 0.88
97 4 0.05
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCCAGTAAGTTAAGACACAATATTTCA
AAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:12990 original size:59 final size:57
Alignment explanation
Indices: 12871--13246 Score: 301
Period size: 59 Copynumber: 6.5 Consensus size: 57
12861 ATCGGGGTTA
*
12871 AAAATGGAATTTTTAGACA-TTCGGGGTAAAATGGAATTTTTGG-AGTTTCGAGGTCG
1 AAAATGGAATTTTTAGA-AGTTCGGGGAAAAATGGAATTTTTGGAAGTTTCGAGGTCG
* * * * * *
12927 AAAATAGAGTTTTTGGACA-TTCGGAGGCAAAAATGGAATTTTTGGGAGTTACGGGGTCG
1 AAAATGGAATTTTTAGA-AGTTCGG-GG-AAAAATGGAATTTTTGGAAGTTTCGAGGTCG
12986 AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC-
1 AAAATGGAATTTTTAGAAGTTCG-GGG-AAAAATGGAATTTTTGGAAGTTTCGAGGTCG
* * *
13044 AAAATTGGAATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAG-TTCG-GG-GG
1 AAAA-TGGAATTTTTAGAAGTTC-GGGGAAAAATGGAATTTTTGGAAGTTTCGAGGTCG
* * *
13100 TAAAATGGAATTTTT-GTAAGTTTCGAGGTCG-AAAATGAAATTTTTGGAAG-TTCGGGGGT-A
1 -AAAATGGAATTTTTAG-AAG-TTCG-GG--GAAAAATGGAATTTTTGGAAGTTTC-GAGGTCG
* * * **
13160 AAAATAGAATTTTTTGAAGTTTCGGGGTCGAAAATGGAATTTTT-GAGAG-TTCGAGGGTAA
1 AAAATGGAATTTTTAGAAG-TTCGGGG--AAAAATGGAATTTTTGGA-AGTTTCGA-GGTCG
* *
13220 AAAATGGAATTTTTGGAAGTTCAGGGA
1 AAAATGGAATTTTTAGAAGTTCGGGGA
13247 CCTCCAGGGC
Statistics
Matches: 271, Mismatches: 25, Indels: 47
0.79 0.07 0.14
Matches are distributed among these distances:
55 1 0.00
56 38 0.14
57 15 0.06
58 66 0.24
59 128 0.47
60 23 0.08
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (57 bp):
AAAATGGAATTTTTAGAAGTTCGGGGAAAAATGGAATTTTTGGAAGTTTCGAGGTCG
Found at i:12992 original size:30 final size:29
Alignment explanation
Indices: 12862--13241 Score: 356
Period size: 29 Copynumber: 13.1 Consensus size: 29
12852 TTGGGAAAAA
** *
12862 TCGGGGTTAAAAATGGAATTTTTAGACA-T
1 TCGGGGTCGAAAATGGAATTTTTGGA-AGT
12891 TCGGGGT--AAAATGGAATTTTTGG-AGTT
1 TCGGGGTCGAAAATGGAATTTTTGGAAG-T
* * *
12918 TCGAGGTCGAAAATAGAGTTTTTGGACA-T
1 TCGGGGTCGAAAATGGAATTTTTGGA-AGT
* *
12947 TCGGAGG-CAAAAATGGAATTTTTGGGAGT
1 TCGG-GGTCGAAAATGGAATTTTTGGAAGT
*
12976 TACGGGGTCGAAAATGGAATTTTTAGAAGT
1 T-CGGGGTCGAAAATGGAATTTTTGGAAGT
*
13006 TCGAGGGT-AAAAATGGAATTTTTGGAAGTT
1 TCG-GGGTCGAAAATGGAATTTTTGGAAG-T
*
13036 TCGAGGTC-AAAATTGGAATTTTTGGAAGT
1 TCGGGGTCGAAAA-TGGAATTTTTGGAAGT
13065 TCGGGG--GTAAAATGGAATTTTTGGAAGT
1 TCGGGGTCG-AAAATGGAATTTTTGGAAGT
*
13093 TCGGGG--GTAAAATGGAATTTTTGTAAGTT
1 TCGGGGTCG-AAAATGGAATTTTTGGAAG-T
* *
13122 TCGAGGTCGAAAATGAAATTTTTGGAAGT
1 TCGGGGTCGAAAATGGAATTTTTGGAAGT
* * *
13151 TCGGGGGT-AAAAATAGAATTTTTTGAAGTT
1 TC-GGGGTCGAAAATGGAATTTTTGGAAG-T
13181 TCGGGGTCGAAAATGGAATTTTT-GAGAGT
1 TCGGGGTCGAAAATGGAATTTTTGGA-AGT
**
13210 TCGAGGGTAAAAAATGGAATTTTTGGAAGT
1 TCG-GGGTCGAAAATGGAATTTTTGGAAGT
13240 TC
1 TC
13242 AGGGACCTCC
Statistics
Matches: 297, Mismatches: 29, Indels: 49
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.00
27 22 0.07
28 43 0.14
29 117 0.39
30 110 0.37
31 4 0.01
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (29 bp):
TCGGGGTCGAAAATGGAATTTTTGGAAGT
Found at i:13245 original size:29 final size:29
Alignment explanation
Indices: 12862--13241 Score: 372
Period size: 30 Copynumber: 13.1 Consensus size: 29
12852 TTGGGAAAAA
* *
12862 TCGGGGTTAAAAATGGAATTTTTAGACA-T
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGT
12891 TCGGGGT--AAAATGGAATTTTTGG-AGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAG-T
* * * *
12918 TCGAGGTCGAAAATAGAGTTTTTGGACA-T
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGT
*
12947 TCGGAGG-CAAAAATGGAATTTTTGGGAGT
1 TCGG-GGTCAAAAATGGAATTTTTGGAAGT
* *
12976 TACGGGGTCGAAAATGGAATTTTTAGAAGT
1 T-CGGGGTCAAAAATGGAATTTTTGGAAGT
13006 TCGAGGGT-AAAAATGGAATTTTTGGAAGTT
1 TCG-GGGTCAAAAATGGAATTTTTGGAAG-T
* *
13036 TCGAGGTCAAAATTGGAATTTTTGGAAGT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGT
13065 TCGGGGGT--AAAATGGAATTTTTGGAAGT
1 TC-GGGGTCAAAAATGGAATTTTTGGAAGT
*
13093 TCGGGGGT--AAAATGGAATTTTTGTAAGTT
1 TC-GGGGTCAAAAATGGAATTTTTGGAAG-T
* * *
13122 TCGAGGTCGAAAATGAAATTTTTGGAAGT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGT
* *
13151 TCGGGGGT-AAAAATAGAATTTTTTGAAGTT
1 TC-GGGGTCAAAAATGGAATTTTTGGAAG-T
*
13181 TCGGGGTCGAAAATGGAATTTTT-GAGAGT
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGT
*
13210 TCGAGGGTAAAAAATGGAATTTTTGGAAGT
1 TCG-GGGTCAAAAATGGAATTTTTGGAAGT
13240 TC
1 TC
13242 AGGGACCTCC
Statistics
Matches: 297, Mismatches: 31, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
25 1 0.00
27 22 0.07
28 50 0.17
29 103 0.35
30 118 0.40
31 3 0.01
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (29 bp):
TCGGGGTCAAAAATGGAATTTTTGGAAGT
Found at i:14260 original size:17 final size:17
Alignment explanation
Indices: 14235--14305 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
14225 GACTTTTTAA
* **
14235 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
14252 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
* *
14269 TTAAATTTAAAACAAAT
1 TTAAATTTTAAATAAAT
*
14286 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
14304 TT
1 TT
14306 GAATCAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 35 0.78
18 10 0.22
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:14264 original size:6 final size:6
Alignment explanation
Indices: 14250--14296 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
14240 TTTTAAATCC
* **
14250 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
14296 A
1 A
14297 AATAAATTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:16786 original size:53 final size:53
Alignment explanation
Indices: 16706--16821 Score: 232
Period size: 53 Copynumber: 2.2 Consensus size: 53
16696 CTTTTTCCTA
16706 AATTTTCAATCAAGTCCTTCTCGTACTCTTAATTATTTTTAAATTGGCCCAAT
1 AATTTTCAATCAAGTCCTTCTCGTACTCTTAATTATTTTTAAATTGGCCCAAT
16759 AATTTTCAATCAAGTCCTTCTCGTACTCTTAATTATTTTTAAATTGGCCCAAT
1 AATTTTCAATCAAGTCCTTCTCGTACTCTTAATTATTTTTAAATTGGCCCAAT
16812 AATTTTCAAT
1 AATTTTCAAT
16822 GCTTTTTAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (53 bp):
AATTTTCAATCAAGTCCTTCTCGTACTCTTAATTATTTTTAAATTGGCCCAAT
Done.