Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015378.1 Kokia drynarioides strain JFW-HI SEQ_130425, 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: 109524
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:7525 original size:13 final size:13
Alignment explanation
Indices: 7507--7534 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7497 TGAACCTTCC
7507 TTTTATATATAAT
1 TTTTATATATAAT
7520 TTTTATATATAAT
1 TTTTATATATAAT
7533 TT
1 TT
7535 ATAGATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTATATATAAT
Found at i:15414 original size:43 final size:42
Alignment explanation
Indices: 15393--15655 Score: 375
Period size: 43 Copynumber: 6.2 Consensus size: 42
15383 TATTTATAGT
15393 GGCGTTTGTGGAGTAAGCGCCGCTAAAGACCATGTTCTTTAGC
1 GGCGTTTGTGG-GTAAGCGCCGCTAAAGACCATGTTCTTTAGC
* *
15436 GGCGTTTGCGGG-AGAGCGCCGCTAAATACCATGTTCTTTAGC
1 GGCGTTTGTGGGTA-AGCGCCGCTAAAGACCATGTTCTTTAGC
* * *
15478 GGCGTTTGTGGGTAAAGCGTCGCTAAAGACCATATTCTTTAGT
1 GGCGTTTGTGGGT-AAGCGCCGCTAAAGACCATGTTCTTTAGC
*
15521 GGCGTTTGTGGGTGAAGCCCCGCTAAAGACCATGTTCTTTAGC
1 GGCGTTTGTGGGT-AAGCGCCGCTAAAGACCATGTTCTTTAGC
* *
15564 GGCGTTTGTGGGGTAAGCGCCGCTAAAGACTATGTTCTTTAGT
1 GGCGTTTGT-GGGTAAGCGCCGCTAAAGACCATGTTCTTTAGC
* * *
15607 GGTGTTTGTGGGTAAGCGCCTCTGAAGACCATGTTCTTTAGC
1 GGCGTTTGTGGGTAAGCGCCGCTAAAGACCATGTTCTTTAGC
15649 GGCGTTT
1 GGCGTTT
15656 TTTCTTATAA
Statistics
Matches: 195, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 74 0.38
43 115 0.59
44 5 0.03
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (42 bp):
GGCGTTTGTGGGTAAGCGCCGCTAAAGACCATGTTCTTTAGC
Found at i:15574 original size:86 final size:85
Alignment explanation
Indices: 15393--15655 Score: 386
Period size: 85 Copynumber: 3.1 Consensus size: 85
15383 TATTTATAGT
* * *
15393 GGCGTTTGTGGAGTAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGCGGGAG-AGCGCCG
1 GGCGTTTGTGG-GTAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGTGAAGCGCCG
*
15457 CTAAATACCATGTTCTTTAGC
65 CTAAAGACCATGTTCTTTAGC
* * *
15478 GGCGTTTGTGGGTAAAGCGTCGCTAAAGACCATATTCTTTAGTGGCGTTTGTGGGTGAAGCCCCG
1 GGCGTTTGTGGGT-AAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGTGAAGCGCCG
15543 CTAAAGACCATGTTCTTTAGC
65 CTAAAGACCATGTTCTTTAGC
* * *
15564 GGCGTTTGTGGGGTAAGCGCCGCTAAAGACTATGTTCTTTAGTGGTGTTTGTGGGT-AAGCGCCT
1 GGCGTTTGT-GGGTAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGTGAAGCGCCG
*
15628 CTGAAGACCATGTTCTTTAGC
65 CTAAAGACCATGTTCTTTAGC
15649 GGCGTTT
1 GGCGTTT
15656 TTTCTTATAA
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
84 2 0.01
85 82 0.51
86 73 0.45
87 4 0.02
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (85 bp):
GGCGTTTGTGGGTAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGTGAAGCGCCGC
TAAAGACCATGTTCTTTAGC
Found at i:15624 original size:128 final size:128
Alignment explanation
Indices: 15344--15655 Score: 389
Period size: 128 Copynumber: 2.4 Consensus size: 128
15334 ATCTGTTAAT
* * ** * * * *
15344 TTTAGCGGTGTTTGCGGAAAAAACGCCGTTAAAGAACACTATT-TATAGTGGCGTTTGTGGAGTA
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGACCA-TATTCTTTAGTGGCGTTTGTGGAGTA
* *
15408 AGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGCGGGAGAGCGCCGCTAAATACCATGTTC
65 AGCCCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGCGGGAGAGCGCCGCTAAAGACCATGTTC
*
15472 TTTAGCGGCGTTTGTGGGTAAAGCGTCGCTAAAGACCATATTCTTTAGTGGCGTTTGTGG-GTGA
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGACCATATTCTTTAGTGGCGTTTGTGGAGT-A
* *
15536 AGCCCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGG-GTAAGCGCCGCTAAAGACTATGTT
65 AGCCCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGCGGGAG--AGCGCCGCTAAAGACCATGTT
15600 C
128 C
* * * * * *
15601 TTTAGTGGTGTTTGTGGGT-AAGCGCCTCTGAAGACCATGTTCTTTAGCGGCGTTT
1 TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGACCATATTCTTTAGTGGCGTTT
15656 TTTCTTATAA
Statistics
Matches: 160, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
127 7 0.04
128 116 0.73
129 37 0.23
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (128 bp):
TTTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGACCATATTCTTTAGTGGCGTTTGTGGAGTAA
GCCCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGCGGGAGAGCGCCGCTAAAGACCATGTTC
Found at i:43976 original size:4 final size:4
Alignment explanation
Indices: 43967--43994 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
43957 AAAACATGAA
43967 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
43995 TGAAAGTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:44508 original size:29 final size:29
Alignment explanation
Indices: 44475--44537 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
44465 TAAATAAATG
*
44475 TTAAAACTTTAAAAC-TTAAATTCGAGATC
1 TTAAAAC-TTAAAACTTTAAATTCAAGATC
* * *
44504 TTAAATCTTAAATCTTTAAATTCAATATC
1 TTAAAACTTAAAACTTTAAATTCAAGATC
44533 TTAAA
1 TTAAA
44538 TTTGAGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (29 bp):
TTAAAACTTAAAACTTTAAATTCAAGATC
Found at i:44518 original size:14 final size:14
Alignment explanation
Indices: 44489--44539 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
44479 AACTTTAAAA
* *
44489 CTTAAATTCGAGAT
1 CTTAAATTCAATAT
*
44503 CTTAAATCTTAA-AT
1 CTTAAAT-TCAATAT
44517 CTTTAAATTCAATAT
1 C-TTAAATTCAATAT
44532 CTTAAATT
1 CTTAAATT
44540 TGAGGGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (14 bp):
CTTAAATTCAATAT
Found at i:44968 original size:2 final size:2
Alignment explanation
Indices: 44961--45000 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44951 ACAAAAATTC
44961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45001 TTAAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50299 original size:46 final size:46
Alignment explanation
Indices: 50232--50319 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
50222 TTTATTGGCC
50232 TAATAACAAATTTAGTATTTCAATGTTTATACATTCCATCAAGGCT
1 TAATAACAAATTTAGTATTTCAATGTTTATACATTCCATCAAGGCT
*
50278 TAATAACAAATTTAGTATTTCAATGTTTATACATTTCATCAA
1 TAATAACAAATTTAGTATTTCAATGTTTATACATTCCATCAA
50320 ATTGATCGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (46 bp):
TAATAACAAATTTAGTATTTCAATGTTTATACATTCCATCAAGGCT
Found at i:51342 original size:20 final size:21
Alignment explanation
Indices: 51319--51358 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
51309 GTAAATATAA
*
51319 AATTATTTTTTA-AAATTTTT
1 AATTATATTTTATAAATTTTT
51339 AATTATATTTTATAAATTTT
1 AATTATATTTTATAAATTTT
51359 AGAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTATATTTTATAAATTTTT
Found at i:51354 original size:22 final size:19
Alignment explanation
Indices: 51319--51358 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
51309 GTAAATATAA
51319 AATTATTTTTTAAAATTTTT
1 AATTATTTTTT-AAATTTTT
51339 AATTATATTTTATAAATTTT
1 AATTAT-TTTT-TAAATTTT
51359 AGAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 11 0.61
22 1 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTATTTTTTAAATTTTT
Found at i:51364 original size:22 final size:20
Alignment explanation
Indices: 51319--51365 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
51309 GTAAATATAA
* *
51319 AATTATTTTTTAAAATTTTT
1 AATTATATTTTAAAATTTTG
51339 AATTATATTTTATAAATTTTAG
1 AATTATATTTTA-AAATTTT-G
51361 AATTA
1 AATTA
51366 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 7 0.30
22 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
AATTATATTTTAAAATTTTG
Found at i:52673 original size:29 final size:30
Alignment explanation
Indices: 52610--52676 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
52600 AATTTGTGTT
*
52610 TAAATTATATTTTTATATTTTATTATATTA
1 TAAATTATATTTTAATATTTTATTATATTA
*
52640 T-AATTATCTTTATAATATTTTA-TAT-TTA
1 TAAATTATATTT-TAATATTTTATTATATTA
52668 TAAATTATA
1 TAAATTATA
52677 ATATGAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.12
29 18 0.56
30 10 0.31
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
TAAATTATATTTTAATATTTTATTATATTA
Found at i:57479 original size:27 final size:27
Alignment explanation
Indices: 57444--57498 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
57434 CAAAAAATAA
*
57444 TATGCTTTGCTATATCACTTGTCTCAC
1 TATGCTTTGCTACATCACTTGTCTCAC
*
57471 TATGTTTTGCTACATCACTTGTCTCAC
1 TATGCTTTGCTACATCACTTGTCTCAC
57498 T
1 T
57499 CCACTATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.45
Consensus pattern (27 bp):
TATGCTTTGCTACATCACTTGTCTCAC
Found at i:58226 original size:5 final size:5
Alignment explanation
Indices: 58216--58245 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
58206 TAACTACTCT
58216 AAACA AAACA AAACA AAACA AAACA AAACA
1 AAACA AAACA AAACA AAACA AAACA AAACA
58246 GCCCCTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:59222 original size:20 final size:19
Alignment explanation
Indices: 59199--59240 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
59189 CTTTTAATAA
59199 TTTTAT-GAACTTTTTTATAT
1 TTTTATGGAA-TTTTTTAT-T
*
59219 TTTTTTGGAATTTTTTATT
1 TTTTATGGAATTTTTTATT
59238 TTT
1 TTT
59241 ATTTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (19 bp):
TTTTATGGAATTTTTTATT
Found at i:77878 original size:22 final size:22
Alignment explanation
Indices: 77827--77878 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
77817 CCTTCACCAC
*
77827 TCATATATATATATATGGAAAA
1 TCATATAAATATATATGGAAAA
* * * *
77849 TTAAATAAATTTATATGGAGAA
1 TCATATAAATATATATGGAAAA
77871 TCATATAA
1 TCATATAA
77879 CACAAGAGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.37
Consensus pattern (22 bp):
TCATATAAATATATATGGAAAA
Found at i:89968 original size:20 final size:21
Alignment explanation
Indices: 89939--89978 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
89929 TCCCTGTGCT
*
89939 CAATCGAAATAGAAA-ATTTC
1 CAATCAAAATAGAAATATTTC
*
89959 CAATCAAAATCGAAATATTT
1 CAATCAAAATAGAAATATTT
89979 AATGCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (21 bp):
CAATCAAAATAGAAATATTTC
Found at i:102215 original size:21 final size:21
Alignment explanation
Indices: 102191--102243 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
102181 ATTATTCCTG
102191 TAAAAACCTAGGTTTTTCATA
1 TAAAAACCTAGGTTTTTCATA
* *
102212 TAAAACTCCTA-GTTTTTCCTA
1 TAAAA-ACCTAGGTTTTTCATA
* *
102233 TATAAATCTAG
1 TAAAAACCTAG
102244 CTAATTGCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 18 0.72
22 4 0.16
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (21 bp):
TAAAAACCTAGGTTTTTCATA
Done.