Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013095.1 Kokia drynarioides strain JFW-HI SEQ_128113, 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: 427744
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 263 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:393547 original size:18 final size:18
Alignment explanation
Indices: 393524--393577 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
393514 ACACGCTTTT
* *
393524 CTTCTGTCTTGTGGCATG
1 CTTCTGTCTTATGGCACG
* *
393542 CTTCTGCCTTATGGTACG
1 CTTCTGTCTTATGGCACG
393560 CTTCTGTCTTATGGCACG
1 CTTCTGTCTTATGGCACG
393578 TTTTCGTCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (18 bp):
CTTCTGTCTTATGGCACG
Found at i:394092 original size:32 final size:32
Alignment explanation
Indices: 394056--394116 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
394046 ACGTCAACTT
*
394056 ATAAATTAATTACTTTAATTT-AGTAACTCGTG
1 ATAAATTAATTAATTTAATTTGA-TAACTCGTG
394088 ATAAATTAATTAATTTAATTTGATAACTC
1 ATAAATTAATTAATTTAATTTGATAACTC
394117 ATTGATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (32 bp):
ATAAATTAATTAATTTAATTTGATAACTCGTG
Found at i:395001 original size:17 final size:16
Alignment explanation
Indices: 394981--395026 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
394971 AAAATGTAGC
394981 AAAAAAATAACAAAACA
1 AAAAAAATAACAAAA-A
394998 AAAAAAATAA-AAAAA
1 AAAAAAATAACAAAAA
* *
395013 AACAAAATATCAAA
1 AAAAAAATAACAAA
395027 CCAGCAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 9 0.35
16 7 0.27
17 10 0.38
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAAAATAACAAAAA
Found at i:397264 original size:17 final size:16
Alignment explanation
Indices: 397233--397288 Score: 85
Period size: 17 Copynumber: 3.4 Consensus size: 16
397223 TTGGAAATTG
397233 AATTTATTTAAATTTA
1 AATTTATTTAAATTTA
397249 AATTTATTTGAAATTTA
1 AATTTATTT-AAATTTA
*
397266 AATTTATTATAAAATTA
1 AATTTATT-TAAATTTA
397283 AATTTA
1 AATTTA
397289 GAAAGTCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
16 9 0.24
17 27 0.73
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:398095 original size:21 final size:20
Alignment explanation
Indices: 398063--398102 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
398053 GTTTTCAAAA
398063 TTTTTATTAATAATAATAAT
1 TTTTTATTAATAATAATAAT
*
398083 TTTTTTTTAAATAATAATAA
1 TTTTTATT-AATAATAATAA
398103 AAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTATTAATAATAATAAT
Found at i:399311 original size:29 final size:27
Alignment explanation
Indices: 399279--399537 Score: 187
Period size: 29 Copynumber: 8.9 Consensus size: 27
399269 GTCCCTAAAC
*
399279 CTTCTAAAAATTACCATTTTACCCTCGAA
1 CTTCCAAAAA-TACCATTTTACCC-CGAA
* *
399308 CTTCCAAAAATCCCATTTTTGACCCCAAA
1 CTTCCAAAAATACCA-TTTT-ACCCCGAA
*
399337 CCTTCTAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAA-TACCATTTTA-CCCCGAA
* * *
399367 CTTCCGAAAATCCCATTTTTGATCCCGAA
1 CTTCCAAAAATACCA-TTTT-ACCCCGAA
*
399396 CCTTCTAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAA-TACCATTTTA-CCCCGAA
* *
399426 CTTCCAAAAATCCCATTTTTGA-CCCTAA
1 CTTCCAAAAATACCA-TTTT-ACCCCGAA
*
399454 CCTTCTAAAAATCACCATTTTACCCCTGAA
1 -CTTCCAAAAAT-ACCATTTTACCCC-GAA
* *
399484 CTTCCAAAAATCCCATTTTTGACTCCGAA
1 CTTCCAAAAATACCA-TTTT-ACCCCGAA
* * *
399513 CCCTCCAAAACTACCATTTTGCCCC
1 -CTTCCAAAAATACCATTTTACCCC
399538 CGTGCATCCG
Statistics
Matches: 183, Mismatches: 28, Indels: 39
0.73 0.11 0.16
Matches are distributed among these distances:
28 24 0.13
29 87 0.48
30 64 0.35
31 8 0.04
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.30
Consensus pattern (27 bp):
CTTCCAAAAATACCATTTTACCCCGAA
Found at i:399485 original size:58 final size:59
Alignment explanation
Indices: 399276--399539 Score: 406
Period size: 59 Copynumber: 4.5 Consensus size: 59
399266 GAGGTCCCTA
* *
399276 AACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* *
399335 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCGAAAATCCCATTTTTGATCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
399394 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCT
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
399452 AACCTTCTAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACTCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
399511 AACCCTC-CAAAACTACCATTTTGCCCCCG
1 AACCTTCTAAAAATTACCATTTTACCCCCG
399540 TGCATCCGAA
Statistics
Matches: 188, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
58 72 0.38
59 116 0.62
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.30
Consensus pattern (59 bp):
AACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:401657 original size:17 final size:18
Alignment explanation
Indices: 401635--401668 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
401625 CTCAAAATTT
*
401635 CTTT-AATTTTTTAAAAG
1 CTTTAAATTTTCTAAAAG
401652 CTTTAAATTTTCTAAAA
1 CTTTAAATTTTCTAAAA
401669 TTTCTGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (18 bp):
CTTTAAATTTTCTAAAAG
Found at i:403999 original size:23 final size:23
Alignment explanation
Indices: 403967--404056 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
403957 TGTTGCTGTT
*
403967 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
* *
403990 ATTAGTACTTTGCGTACTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
* * *
404013 TTTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
*
404036 -TTAGTACTTTG-GTACTCTCTG
1 ATTAGCACTTTGTGTACTCTCTG
404057 TTTGTTCCGT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 9 0.16
22 9 0.16
23 38 0.68
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (23 bp):
ATTAGCACTTTGTGTACTCTCTG
Found at i:404052 original size:44 final size:46
Alignment explanation
Indices: 403968--404059 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
403958 GTTGCTGTTA
*
403968 TTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGCGTACTCTCTGT
1 TTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGCGTACTCTCTGT
404014 TTAGCACTGTGTGTGCTCTCTG-TTAGTACTTTG-GTACTCTCTGT
1 TTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGCGTACTCTCTGT
404058 TT
1 TT
404060 GTTCCGTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 13 0.29
45 11 0.24
46 21 0.47
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (46 bp):
TTAGCACTGTGTGTGCTCTCTGATTAGTACTTTGCGTACTCTCTGT
Found at i:405900 original size:21 final size:22
Alignment explanation
Indices: 405876--405918 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
405866 TTTAAAAATA
405876 AAATAAAAAAC-AAAAAAATTT
1 AAATAAAAAACTAAAAAAATTT
* * *
405897 AAATGAAGAACTAAAATAATTT
1 AAATAAAAAACTAAAAAAATTT
405919 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (22 bp):
AAATAAAAAACTAAAAAAATTT
Found at i:406850 original size:28 final size:28
Alignment explanation
Indices: 406792--406851 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
406782 TTAAGCTCTC
* * *
406792 AAAAAAAAAAATGAAATGAGATTGACCA
1 AAAAAAAAAAATGAAACGAGAGTGACAA
*
406820 AAAAAAAAAAATGAAACGAGAGTGATAA
1 AAAAAAAAAAATGAAACGAGAGTGACAA
406848 AAAA
1 AAAA
406852 TCTAACAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.68, C:0.05, G:0.15, T:0.12
Consensus pattern (28 bp):
AAAAAAAAAAATGAAACGAGAGTGACAA
Found at i:410977 original size:18 final size:18
Alignment explanation
Indices: 410954--410991 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
410944 GGCTAATGTC
410954 CTAAAAACAACCATCTGT
1 CTAAAAACAACCATCTGT
410972 CTAAAAACAACCATCTGT
1 CTAAAAACAACCATCTGT
410990 CT
1 CT
410992 CTGAAGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (18 bp):
CTAAAAACAACCATCTGT
Found at i:412951 original size:2 final size:2
Alignment explanation
Indices: 412939--412992 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
412929 TTTATAAGTA
412939 AT AT A- 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 AT
412980 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
412993 AAGAAAAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:416978 original size:6 final size:6
Alignment explanation
Indices: 416967--416999 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
416957 TACAAACTAC
*
416967 TGTTCA TGTTCA TGTTCA TGTTCA TGTTGA TGT
1 TGTTCA TGTTCA TGTTCA TGTTCA TGTTCA TGT
417000 ATGTAAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.52
Consensus pattern (6 bp):
TGTTCA
Found at i:418960 original size:6 final size:6
Alignment explanation
Indices: 418949--418975 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
418939 AGTTAAGTTT
418949 GAGAAA GAGAAA GAGAAA GAGAAA GAG
1 GAGAAA GAGAAA GAGAAA GAGAAA GAG
418976 TGATGAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:427489 original size:6 final size:6
Alignment explanation
Indices: 427478--427503 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
427468 TCGGCCTCCA
427478 GGAGGT GGAGGT GGAGGT GGAGGT GG
1 GGAGGT GGAGGT GGAGGT GGAGGT GG
427504 TGCTCCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (6 bp):
GGAGGT
Done.