Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012461.1 Kokia drynarioides strain JFW-HI SEQ_127465, 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: 5419
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:429 original size:16 final size:13
Alignment explanation
Indices: 393--426 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
383 AATAAATGGC
393 ATTAATAAATATT
1 ATTAATAAATATT
406 ATTAATAAATATT
1 ATTAATAAATATT
*
419 AGTAATAA
1 ATTAATAA
427 TAATAAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTAATAAATATT
Found at i:1832 original size:29 final size:29
Alignment explanation
Indices: 1508--1857 Score: 263
Period size: 29 Copynumber: 12.0 Consensus size: 29
1498 CCCTGGAGGT
**
1508 CCCT-AAACTGTCCAAAAATTCTGTTTTTA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTA
** *
1537 CCCTCGAACTT-CAAAAAATCTCATTTTTAA
1 CCCTAAAACTTCCAAAAATTC-CATTTTT-A
*
1567 CCCT-AAACTTCCCAAAATTCCATTTTTTA
1 CCCTAAAACTTCCAAAAATTCCA-TTTTTA
* *
1596 CCCCAAAACTTCCAAAAATCCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
*
1625 CCACCAAAA-TTCCAAAAATTCCA-TTTTA
1 CC-CTAAAACTTCCAAAAATTCCATTTTTA
* * *
1653 ACCTCGAAACTTCTAAAAA-TCGCATTTTTA
1 CCCT-AAAACTTCCAAAAATTC-CATTTTTA
*** *
1683 CCCCCGAACTTCCCAAAATTCCATTTTGT-
1 CCCTAAAACTTCCAAAAATTCCATTTT-TA
* *
1712 -CCTCGAAACTTCCAAAAATCCCATTTTTA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTA
** * * * *
1741 CCCTCGAGCTTCTAAAATTTCCATTCTTAA
1 CCCTAAAACTTCCAAAAATTCCATT-TTTA
*
1771 CCCCAAAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTT-A
1801 CCCTAAAACTTCCAAAAATTACCA-TTTTA
1 CCCTAAAACTTCCAAAAATT-CCATTTTTA
*
1830 CCC-ACAAA-TGTCCAAAAATTCTATTTTT
1 CCCTA-AAACT-TCCAAAAATTCCATTTTT
1858 GACCTCGAAA
Statistics
Matches: 257, Mismatches: 42, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.00
28 26 0.10
29 125 0.49
30 102 0.40
31 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTA
Found at i:1914 original size:58 final size:59
Alignment explanation
Indices: 1548--1944 Score: 184
Period size: 58 Copynumber: 6.8 Consensus size: 59
1538 CCTCGAACTT
* * * * *
1548 CAAAAAATCTCATTTTTAACCCT-AAACTTCCCAAAATT-CCATTTTTTACCCCAAAACT-TC
1 CAAAAAGTC-CATTTTTGACCCTAAAACTTCCAAAAATTACCA-TTTTAACCAC-AAA-TGTC
* *
1608 CAAAAA-TCCCATTTTT-ACCACCAAAA-TTCCAAAAATT-CCATTTTAACCTCGAAACT-TC
1 CAAAAAGT-CCATTTTTGACC-CTAAAACTTCCAAAAATTACCATTTTAACCAC-AAA-TGTC
* *** * ** *
1666 TAAAAA-TCGCATTTTT-ACCCCCGAACTTCCCAAAATT-CCATTTTGTCCTCGAAACT-TC
1 CAAAAAGTC-CATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTAACCAC-AAA-TGTC
** * * * *
1724 CAAAAA-TCCCATTTTT-ACCCTCGAGCTT-CTAAAATTTCCATTCTTAACCCCAAAACT-TC
1 CAAAAAGT-CCATTTTTGACCCTAAAACTTCCAAAAATTACCATT-TTAACCAC-AAA-TGTC
* *
1783 CAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCACAAATGTC
1 CAAAAAGTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTAACCACAAATGTC
* * * * * *
1842 CAAAAATTCTATTTTTGA-CCTCGAAAC-TCTC-AAAATTACCCTTTTAACCTCGAATGTC
1 CAAAAAGTCCATTTTTGACCCT-AAAACTTC-CAAAAATTACCATTTTAACCACAAATGTC
* * * * ** *
1900 TAAATAGTCCATTTTTAACCCCAAATTTTCCCAAAATTACCATTT
1 CAAAAAGTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTT
1945 CACCCCGAGA
Statistics
Matches: 278, Mismatches: 42, Indels: 35
0.78 0.12 0.10
Matches are distributed among these distances:
57 12 0.04
58 136 0.49
59 92 0.33
60 26 0.09
61 12 0.04
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (59 bp):
CAAAAAGTCCATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTAACCACAAATGTC
Found at i:2351 original size:96 final size:96
Alignment explanation
Indices: 2209--2400 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
2199 AAGACTTTAA
* * * **
2209 AATCGAGGTAATATTCTTTAATTTCGAGTTTCGAGAATTTGTGCCTTAACTTACTAGGTGCAATT
1 AATCGAGGCAATATTCTTTAACTTCGAGTTTCGAGAATTTGCGCCTTAACTTACTAGGTGCAACC
2274 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCTTCAAATCGAAATAATCGAATACCCTT
* *
2305 AATCGAGGCAATGTTTCTTTAACTTCGA--TTCTGA-AATATTGCGCCTTAATTTACTAGGTGCA
1 AATCGAGGCAAT-ATTCTTTAACTTCGAGTTTC-GAGAAT-TTGCGCCTTAACTTACTAGGTGCA
* *
2367 ACCTTTCTTCAAATCGAGATAATCGAATATCCTT
63 ACCTTTCTTCAAATCGAAATAATCGAATACCCTT
2401 TTCCCAAAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 6 0.07
96 65 0.77
97 13 0.15
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTAACTTCGAGTTTCGAGAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:3090 original size:30 final size:30
Alignment explanation
Indices: 3068--3127 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3058 ATTTTGACTC
*
3068 TCAAACCTTTCTAAAATCATATTTTAACCT
1 TCAAACCTTTCCAAAATCATATTTTAACCT
*
3098 TCAAACCTTTCCAAAATCACATTTTAACCT
1 TCAAACCTTTCCAAAATCATATTTTAACCT
3128 CATACTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (30 bp):
TCAAACCTTTCCAAAATCATATTTTAACCT
Found at i:3179 original size:29 final size:29
Alignment explanation
Indices: 3105--3213 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 29
3095 CCTTCAAACC
* *
3105 TTTCCAAAATCACATTTTAACCTCATACT
1 TTTCCAAAATTACATTTTAACCCCATACT
* * *
3134 TTTTCAAAACTGA-ATTTTGACCCCATACT
1 TTTCCAAAA-TTACATTTTAACCCCATACT
* * * *
3163 TCTCCAAAATTATATTTTAACCCCTAAATT
1 TTTCCAAAATTACATTTTAACCCC-ATACT
3193 TTTCCAAAATTACATTTTAAC
1 TTTCCAAAATTACATTTTAAC
3214 AATTGCATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 2 0.03
29 39 0.60
30 24 0.37
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTCCAAAATTACATTTTAACCCCATACT
Found at i:3256 original size:30 final size:30
Alignment explanation
Indices: 3219--3524 Score: 256
Period size: 30 Copynumber: 10.4 Consensus size: 30
3209 TTAACAATTG
* * *
3219 CATTTTGACCCTTAAACTTTTCTAAAATTA
1 CATTTTGACCCTCAAACTTTTCCAAAATCA
*
3249 CAATTTGACCC-CTAAACTTTTCCAAAATCA
1 CATTTTGACCCTC-AAACTTTTCCAAAATCA
* * *
3279 TATTTTAACCC-CAAAC-TTCCCTAAAATCA
1 CATTTTGACCCTCAAACTTTTCC-AAAATCA
3308 CATTTTGACCC-CAAA-TTTTCCCAAAATCA
1 CATTTTGACCCTCAAACTTTT-CCAAAATCA
* *
3337 CATTTTAACCCTCAAACATTTCCAAAATCA
1 CATTTTGACCCTCAAACTTTTCCAAAATCA
*
3367 CATTTTCACCCTCAAACTTTTCCAAAA-CTA
1 CATTTTGACCCTCAAACTTTTCCAAAATC-A
** * *
3397 CATTTTGACCC-CAAACTTCCCCAAGATAA
1 CATTTTGACCCTCAAACTTTTCCAAAATCA
* * *
3426 CATTTTGACCCT-AAACCTTCCCAAAATCC
1 CATTTTGACCCTCAAACTTTTCCAAAATCA
*** *
3455 CATTTT-ACCC-CAAACTTTGATAAAATTA
1 CATTTTGACCCTCAAACTTTTCCAAAATCA
* * * *
3483 CCTTTTAACCCTCGAA-TTCTTCCAAAATTA
1 CATTTTGACCCTCAAACTT-TTCCAAAATCA
*
3513 CATTTTAACCCT
1 CATTTTGACCCT
3525 AAATTCTTTG
Statistics
Matches: 226, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
28 24 0.11
29 92 0.41
30 107 0.47
31 3 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.33
Consensus pattern (30 bp):
CATTTTGACCCTCAAACTTTTCCAAAATCA
Found at i:3295 original size:29 final size:29
Alignment explanation
Indices: 3219--3472 Score: 255
Period size: 29 Copynumber: 8.7 Consensus size: 29
3209 TTAACAATTG
* * *
3219 CATTTTGACCCTTAAACTTTTCTAAAATTA
1 CATTTTGACCC-CAAACTTTTCCAAAATCA
*
3249 CAATTTGACCCCTAAACTTTTCCAAAATCA
1 CATTTTGACCCC-AAACTTTTCCAAAATCA
* * *
3279 TATTTTAACCCCAAAC-TTCCCTAAAATCA
1 CATTTTGACCCCAAACTTTTCC-AAAATCA
3308 CATTTTGACCCCAAA-TTTTCCCAAAATCA
1 CATTTTGACCCCAAACTTTT-CCAAAATCA
* *
3337 CATTTTAACCCTCAAACATTTCCAAAATCA
1 CATTTTGACCC-CAAACTTTTCCAAAATCA
*
3367 CATTTTCACCCTCAAACTTTTCCAAAA-CTA
1 CATTTTGACCC-CAAACTTTTCCAAAATC-A
** * *
3397 CATTTTGACCCCAAACTTCCCCAAGATAA
1 CATTTTGACCCCAAACTTTTCCAAAATCA
* * * *
3426 CATTTTGACCCTAAACCTTCCCAAAATCC
1 CATTTTGACCCCAAACTTTTCCAAAATCA
3455 CATTTT-ACCCCAAACTTT
1 CATTTTGACCCCAAACTTT
3473 GATAAAATTA
Statistics
Matches: 188, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
28 14 0.07
29 86 0.46
30 85 0.45
31 3 0.02
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
CATTTTGACCCCAAACTTTTCCAAAATCA
Found at i:3384 original size:118 final size:116
Alignment explanation
Indices: 3219--3523 Score: 339
Period size: 118 Copynumber: 2.6 Consensus size: 116
3209 TTAACAATTG
* * * *
3219 CATTTTGACCCTTAAACTTTTCTAAAATTACAATTTGACCC-CTAAACTTTTCCAAAATCATATT
1 CATTTT-ACCCTCAAAC-TTTCTAAAATTACATTTTAACCCTC-AAACTTTTCCAAAATCACATT
* * **
3283 TTAACCCCAAACTTCCCTAAAATCACATTTTGACCCCAAATTTTCCCAAAATCA
63 TTAACCCCAAACTTCCCCAAAATAACATTTTGACCCCAAACCTTCCCAAAATCA
* * *
3337 CATTTTAACCCTCAAACATTTCCAAAATCACATTTTCACCCTCAAACTTTTCCAAAA-CTACATT
1 CATTTT-ACCCTCAAAC-TTTCTAAAATTACATTTTAACCCTCAAACTTTTCCAAAATC-ACATT
* * * *
3401 TTGACCCCAAACTTCCCCAAGATAACATTTTGACCCTAAACCTTCCCAAAATCC
63 TTAACCCCAAACTTCCCCAAAATAACATTTTGACCCCAAACCTTCCCAAAATCA
* * * *
3455 CATTTTACCC-CAAACTTTGATAAAATTACCTTTTAACCCTCGAA-TTCTTCCAAAATTACATTT
1 CATTTTACCCTCAAACTTT-CTAAAATTACATTTTAACCCTCAAACTT-TTCCAAAATCACATTT
3518 TAACCC
64 TAACCC
3524 TAAATTCTTT
Statistics
Matches: 158, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
115 5 0.03
116 43 0.27
117 5 0.03
118 104 0.66
119 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (116 bp):
CATTTTACCCTCAAACTTTCTAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTA
ACCCCAAACTTCCCCAAAATAACATTTTGACCCCAAACCTTCCCAAAATCA
Done.