Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008458.1 Kokia drynarioides strain JFW-HI SEQ_123133, 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: 20406
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:404 original size:29 final size:29
Alignment explanation
Indices: 358--686 Score: 203
Period size: 30 Copynumber: 11.2 Consensus size: 29
348 CCTAAAAGGT
* *
358 CCCT-AAACTATCCAAAAATCATATTTTGA
1 CCCTCAAACT-TCCAAAAATTACATTTTGA
*
387 CCCTCAAACTTCTCAAAAATTACATTTTCA
1 CCCTCAAACTTC-CAAAAATTACATTTTGA
**
417 CCCTTGAACTTCCAAAAATTACATTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTGA
*
446 CCC-CTAAACTTTCCAAAAAATACATTTTGA
1 CCCTC-AAAC-TTCCAAAAATTACATTTTGA
*
476 CCC-CTAAACTTCCAAAAATTATAATTTT-A
1 CCCTC-AAACTTCCAAAAATTA-CATTTTGA
** *
505 CCCTTTAACTTTCC-AAAATTACGTATTTGA
1 CCCTCAAAC-TTCCAAAAATTACAT-TTTGA
* * *
535 CCAT-AAATTTCTCAAAAATTACATTTTAA
1 CCCTCAAACTTC-CAAAAATTACATTTTGA
* ** * * *
564 CCCCCAAACTTTCC-CGAATTCCCTTTTTAA
1 CCCTCAAAC-TTCCAAAAATT-ACATTTTGA
**
594 CCCTCGAATTTTCCAAAAATTACCATTTT-A
1 CCCTC-AAACTTCCAAAAATTA-CATTTTGA
* * * *
624 CCTTCGAACGTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACA-TTTTGA
*
654 --CTCGAAACTTTCAAAAAATTACATTTT-A
1 CCCTC-AAAC-TTCCAAAAATTACATTTTGA
682 CCCTC
1 CCCTC
687 GAATGTTTGA
Statistics
Matches: 232, Mismatches: 45, Indels: 45
0.72 0.14 0.14
Matches are distributed among these distances:
28 9 0.04
29 91 0.39
30 118 0.51
31 14 0.06
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTGA
Found at i:463 original size:59 final size:59
Alignment explanation
Indices: 361--577 Score: 219
Period size: 59 Copynumber: 3.7 Consensus size: 59
351 AAAAGGTCCC
* * * *
361 TAAACTATCCAAAAATCATATTTTGA-CCCTCAAAC-TTCTCAAAAATTACATTTTCACCCT
1 TAAACT-TCCAAAAATTACATTTTGACCCCT-AAACTTTC-CAAAAATTACATTTTGACCCA
* * *
421 TGAACTTCCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAAATACATTTTGACCCC
1 TAAACTTCCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTACATTTTGACCCA
* * * *
480 TAAACTTCCAAAAATTATAATTTT-ACCCTTTAACTTTCC-AAAATTACGTATTTGA-CCA
1 TAAACTTCCAAAAATTA-CATTTTGACCCCTAAACTTTCCAAAAATTACAT-TTTGACCCA
* * *
538 TAAATTTCTCAAAAATTACATTTTAACCCCCAAACTTTCC
1 TAAACTTC-CAAAAATTACATTTTGACCCCTAAACTTTCC
578 CGAATTCCCT
Statistics
Matches: 133, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
58 22 0.17
59 94 0.71
60 17 0.13
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (59 bp):
TAAACTTCCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAATTACATTTTGACCCA
Found at i:679 original size:58 final size:60
Alignment explanation
Indices: 587--768 Score: 183
Period size: 60 Copynumber: 3.0 Consensus size: 60
577 CCGAATTCCC
* * * *
587 TTTTTAACCCTCGAATTTTCCAAAAATTACCATTTTACCTTCGAACGTCCAAAAATTCCA-
1 TTTTTGACCCT-GAAATTTCAAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTCCAT
* * ***
647 TTTTTGACTC-GAAACTTTCAAAAAATTA-CATTTTACCCTCGAATGTTTGAAAATTCCAT
1 TTTTTGACCCTGAAA-TTTCAAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTCCAT
* * * * *
706 TTTTTTACCCTGAAATTTCAAAAAATTACCATTTTATCCC-CGAATGTCTAAAATTTTCAT
1 TTTTTGACCCTGAAATTTCAAAAAATTACCATTTTA-CCCTCGAACGTCCAAAAATTCCAT
766 TTT
1 TTT
769 CAACCCGAAC
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
58 28 0.27
59 33 0.32
60 38 0.37
61 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (60 bp):
TTTTTGACCCTGAAATTTCAAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTCCAT
Found at i:725 original size:59 final size:58
Alignment explanation
Indices: 580--802 Score: 204
Period size: 59 Copynumber: 3.8 Consensus size: 58
570 AACTTTCCCG
* * * * * *
580 AATTCCCTTTTTAACCCTCGAATTTTCCAAAAATTACCATTTTACCTTCGAACGTCCAAA
1 AATTCCATTTTTAACCCT-GAAATTTCAAAAAATTACCATTTTACCCTCGAATGT-CTAA
* * *
640 AATTCCATTTTTGACTC-GAAACTTTCAAAAAATTA-CATTTTACCCTCGAATGTTTGAA
1 AATTCCATTTTTAACCCTGAAA-TTTCAAAAAATTACCATTTTACCCTCGAATGTCT-AA
*
698 AATTCCATTTTTTTACCCTGAAATTTCAAAAAATTACCATTTTATCCC-CGAATGTCTAA
1 AATTCCA-TTTTTAACCCTGAAATTTCAAAAAATTACCATTTTA-CCCTCGAATGTCTAA
* * * ** *
757 AATTTTCATTTTCAACCC-G-AACTTCCCAAAATTACTATTTTACCCT
1 AA-TTCCATTTTTAACCCTGAAATTTCAAAAAATTACCATTTTACCCT
803 TGGGTACCCA
Statistics
Matches: 136, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
56 3 0.02
57 19 0.14
58 29 0.21
59 45 0.33
60 37 0.27
61 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (58 bp):
AATTCCATTTTTAACCCTGAAATTTCAAAAAATTACCATTTTACCCTCGAATGTCTAA
Found at i:741 original size:29 final size:30
Alignment explanation
Indices: 380--740 Score: 152
Period size: 30 Copynumber: 12.2 Consensus size: 30
370 CAAAAATCAT
* *
380 ATTTTGACCCTCAAACTTCTCAAAAATTA-C
1 ATTTTGACCCTGAAATTTC-CAAAAATTACC
* *
410 ATTTTCACCCTTG-AACTTCCAAAAATTA-C
1 ATTTTGACCC-TGAAATTTCCAAAAATTACC
*
439 ATTTTGACCCCT-AAACTTTCCAAAAAATA-C
1 ATTTTGA-CCCTGAAA-TTTCCAAAAATTACC
* **
469 ATTTTGACCCCT-AAACTTCCAAAAATTATA
1 ATTTTGA-CCCTGAAATTTCCAAAAATTACC
* *
499 ATTTT-ACCCTTTAACTTTCC-AAAATTA-C
1 ATTTTGACCC-TGAAATTTCCAAAAATTACC
* *
527 GTATTTGACCAT-AAATTTCTCAAAAATTA-C
1 AT-TTTGACCCTGAAATTTC-CAAAAATTACC
* ** ** *
557 ATTTTAACCCCCAAACTTTCC-CGAATTCCC
1 ATTTTGACCCTGAAA-TTTCCAAAAATTACC
* * *
587 TTTTTAACCCTCGAATTTTCCAAAAATTACC
1 ATTTTGACCCT-GAAATTTCCAAAAATTACC
* **
618 ATTTT-ACCTTCG-AACGTCCAAAAATT-CC
1 ATTTTGACCCT-GAAATTTCCAAAAATTACC
* *
646 ATTTTTGACTC-GAAACTTTCAAAAAATTA-C
1 A-TTTTGACCCTGAAA-TTTCCAAAAATTACC
**
676 ATTTT-ACCCTCG-AATGTT-TGAAAATT-CC
1 ATTTTGACCCT-GAAAT-TTCCAAAAATTACC
* *
704 ATTTTTTTACCCTGAAATTTCAAAAAATTACC
1 A--TTTTGACCCTGAAATTTCCAAAAATTACC
736 ATTTT
1 ATTTT
741 ATCCCCGAAT
Statistics
Matches: 257, Mismatches: 43, Indels: 62
0.71 0.12 0.17
Matches are distributed among these distances:
28 26 0.10
29 79 0.31
30 118 0.46
31 31 0.12
32 3 0.01
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
ATTTTGACCCTGAAATTTCCAAAAATTACC
Found at i:8098 original size:44 final size:44
Alignment explanation
Indices: 8043--8254 Score: 254
Period size: 46 Copynumber: 4.8 Consensus size: 44
8033 AGACACACCG
8043 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATTCCA
1 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATTCCA
* * * *
8087 ATCTATTACCCCTAAGTCAAGAGGGGCAAATTAAAGCCACCATCCA
1 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCA--TTCCA
*
8133 ATCTTTTACCCTTAAGTCAAGAGGGGCAGATT-ACAGCCATCATCCA
1 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGA-AGCCAT--TCCA
* * *
8179 ATCTTTTACTCCTAA-TCAAAAGGGGTAGATTGAAG--ATTCCA
1 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATTCCA
* *
8220 ATCTTTTACCCTTAA-TCAAGAGGGGTAGATTGAAG
1 ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAG
8255 ATTTCAAGAG
Statistics
Matches: 147, Mismatches: 15, Indels: 15
0.83 0.08 0.08
Matches are distributed among these distances:
41 36 0.24
43 2 0.01
44 36 0.24
45 17 0.12
46 56 0.38
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (44 bp):
ATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCATTCCA
Found at i:8261 original size:23 final size:23
Alignment explanation
Indices: 8235--8284 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
8225 TTACCCTTAA
*
8235 TCAAGAGGGGTAGATTGAAGATT
1 TCAAGAGAGGTAGATTGAAGATT
8258 TCAAGAGAGGTAGATTGAAGATT
1 TCAAGAGAGGTAGATTGAAGATT
8281 TCAA
1 TCAA
8285 TCTTTTACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.30, T:0.26
Consensus pattern (23 bp):
TCAAGAGAGGTAGATTGAAGATT
Found at i:8303 original size:64 final size:64
Alignment explanation
Indices: 8202--8321 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
8192 AATCAAAAGG
*
8202 GGTAGATTGAAGATTCCAATCTTTTACCCTTAATCAAGAGGGGTAGATTGAAGATTTCAAGAGA
1 GGTAGATTGAAGATTCCAATCTTTTACCCTTAATCAAGAAGGGTAGATTGAAGATTTCAAGAGA
* *
8266 GGTAGATTGAAGATTTCAATCTTTTACCGTTAATCAAGAAGGGTAGATTGAAGATT
1 GGTAGATTGAAGATTCCAATCTTTTACCCTTAATCAAGAAGGGTAGATTGAAGATT
8322 CCAGTCTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (64 bp):
GGTAGATTGAAGATTCCAATCTTTTACCCTTAATCAAGAAGGGTAGATTGAAGATTTCAAGAGA
Found at i:8349 original size:41 final size:43
Alignment explanation
Indices: 8258--8390 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 43
8248 ATTGAAGATT
* * * * *
8258 TCAAG-AGAGGTAGATTGAAGATTTCAATCTTTTA-CCGTTAA
1 TCAAGAAGGGGTAGATTGAAGATTCCAGTCTTTTACCCCTAAA
8299 TCAAGAA-GGGTAGATTGAAGATTCCAGTCTTTTACCCCTAAA
1 TCAAGAAGGGGTAGATTGAAGATTCCAGTCTTTTACCCCTAAA
* * *
8341 TTAA-AAGGGGCAAATTGAAGACCATTCC-GATCTTTTACCCCT-AA
1 TCAAGAAGGGGTAGATTGAAG---ATTCCAG-TCTTTTACCCCTAAA
8385 TCAAGA
1 TCAAGA
8391 GGAGCAGATC
Statistics
Matches: 75, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
41 31 0.41
42 20 0.27
44 6 0.08
45 18 0.24
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (43 bp):
TCAAGAAGGGGTAGATTGAAGATTCCAGTCTTTTACCCCTAAA
Found at i:9056 original size:23 final size:23
Alignment explanation
Indices: 9030--9084 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
9020 CTAATTACAA
*
9030 AAACCCAAAATATAAACAGATCC
1 AAACCCAAAACATAAACAGATCC
* * * *
9053 AAACCTAAACCCTAAACAGATCT
1 AAACCCAAAACATAAACAGATCC
9076 AAACCCAAA
1 AAACCCAAA
9085 CCAAGTTGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.29, G:0.04, T:0.13
Consensus pattern (23 bp):
AAACCCAAAACATAAACAGATCC
Found at i:9085 original size:23 final size:23
Alignment explanation
Indices: 9042--9086 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9032 ACCCAAAATA
*
9042 TAAACAGATCCAAACCTAAACCC
1 TAAACAGATCCAAACCCAAACCC
*
9065 TAAACAGATCTAAACCCAAACC
1 TAAACAGATCCAAACCCAAACC
9087 AAGTTGGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.33, G:0.04, T:0.13
Consensus pattern (23 bp):
TAAACAGATCCAAACCCAAACCC
Found at i:11842 original size:8 final size:9
Alignment explanation
Indices: 11817--11885 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 9
11807 AAATAATGAA
11817 AATTTTTAGT
1 AATTTTTA-T
11827 AAATTTTTAT
1 -AATTTTTAT
11837 -ATTTTT-T
1 AATTTTTAT
11844 AATTTTT-T
1 AATTTTTAT
*
11852 AATTTTAAT
1 AATTTTTAT
*
11861 AATTTTTGT
1 AATTTTTAT
11870 AATATTTTAT
1 AAT-TTTTAT
11880 -ATTTTT
1 AATTTTT
11886 TGCAATTCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
7 1 0.02
8 23 0.45
9 13 0.25
10 6 0.12
11 8 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
AATTTTTAT
Found at i:11844 original size:9 final size:8
Alignment explanation
Indices: 11830--11886 Score: 60
Period size: 9 Copynumber: 6.6 Consensus size: 8
11820 TTTTAGTAAA
11830 TTTTTATAT
1 TTTTTA-AT
11839 TTTTTAAT
1 TTTTTAAT
11847 TTTTTAAT
1 TTTTTAAT
*
11855 TTTAATAAT
1 TTT-TTAAT
11864 TTTTGTAAT
1 TTTT-TAAT
*
11873 ATTTTATAT
1 TTTTTA-AT
11882 TTTTT
1 TTTTT
11887 GCAATTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 15 0.37
9 26 0.63
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTAAT
Done.