Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009357.1 Kokia drynarioides strain JFW-HI SEQ_124064, 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: 38097
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3855 original size:53 final size:53
Alignment explanation
Indices: 3789--4185 Score: 506
Period size: 53 Copynumber: 7.5 Consensus size: 53
3779 GAATCCTTCT
* * * *
3789 GATGACTCTGTGTCATTGTGACTTATATGAATCCTATTGCGGATTAAAGGTCC
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* * * * * *
3842 GATGACACGGTGTCACCATGAGTTGTATGAATCCTATCACGAATTAAAGGTCC
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* *
3895 AATGACTCGGTGTCATCGTAAGTTATATGAATCCTATTACGGATTAAAGGTCC
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* * * *
3948 GATGACTCAGTGTCATCATGAGTTATTTGAATCCTATTGCGGATTAAAGGTCC
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* * *
4001 GATGACTCTGTGTCATCGTGAGTTGTATGAATCCTATTGCGGATTAAAGGTCC
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* * *
4054 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTCG
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* * ** * *
4107 GATGACTCTGTGTCATCGTGAGTTATATGAACCCTATTACAAATTAAAGTTTC
1 GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
* * * *
4160 GATGACTCCGTGCCATCTTAAGTTAT
1 GATGACTCGGTGTCATCGTGAGTTAT
4186 CAAATGTGAA
Statistics
Matches: 297, Mismatches: 47, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 297 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (53 bp):
GATGACTCGGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTCC
Found at i:9676 original size:33 final size:33
Alignment explanation
Indices: 9623--9772 Score: 124
Period size: 33 Copynumber: 4.5 Consensus size: 33
9613 AGTGTATATA
* *
9623 GATG-TAAGACCAGAGCTGGGCTATGGCATTCT
1 GATGTTAAGACCATAGTTGGGCTATGGCATTCT
*
9655 GATGTTAAGACCATATTTGGGCTATGGCATTCT
1 GATGTTAAGACCATAGTTGGGCTATGGCATTCT
*** * ** *
9688 -AACATAAGACCATGGTTGGATTATGGCAATGTAT
1 GATGTTAAGACCATAGTTGGGCTATGGC-AT-TCT
* * *
9722 ATATATGTAAGACCATAGCTGGGCTATGGCATTCT
1 -GATGT-TAAGACCATAGTTGGGCTATGGCATTCT
*
9757 GGTGTTAAGACCATAG
1 GATGTTAAGACCATAG
9773 ACAGGTTATG
Statistics
Matches: 90, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
32 24 0.27
33 38 0.42
34 4 0.04
35 2 0.02
36 3 0.03
37 19 0.21
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (33 bp):
GATGTTAAGACCATAGTTGGGCTATGGCATTCT
Found at i:9763 original size:102 final size:102
Alignment explanation
Indices: 9587--9771 Score: 316
Period size: 102 Copynumber: 1.8 Consensus size: 102
9577 CTGCCTTTTG
*
9587 ACATAAGACCATGGTTGGACCATGGCAGTGTATATAGATGTAAGACCAGAGCTGGGCTATGGCAT
1 ACATAAGACCATGGTTGGACCATGGCAATGTATATAGATGTAAGACCAGAGCTGGGCTATGGCAT
9652 TCTGATGTTAAGACCATATTTGGGCTATGGCATTCTA
66 TCTGATGTTAAGACCATATTTGGGCTATGGCATTCTA
** * *
9689 ACATAAGACCATGGTTGGATTATGGCAATGTATATATATGTAAGACCATAGCTGGGCTATGGCAT
1 ACATAAGACCATGGTTGGACCATGGCAATGTATATAGATGTAAGACCAGAGCTGGGCTATGGCAT
*
9754 TCTGGTGTTAAGACCATA
66 TCTGATGTTAAGACCATA
9772 GACAGGTTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (102 bp):
ACATAAGACCATGGTTGGACCATGGCAATGTATATAGATGTAAGACCAGAGCTGGGCTATGGCAT
TCTGATGTTAAGACCATATTTGGGCTATGGCATTCTA
Found at i:13543 original size:20 final size:21
Alignment explanation
Indices: 13498--13545 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
13488 GGCCATTGTT
*
13498 TAATGTTTGCCATTCTTTGAC
1 TAATGTTTGACATTCTTTGAC
* *
13519 CAATGTTTGACA-TCTTTGGC
1 TAATGTTTGACATTCTTTGAC
13539 TAATGTT
1 TAATGTT
13546 AGATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (21 bp):
TAATGTTTGACATTCTTTGAC
Found at i:14048 original size:98 final size:97
Alignment explanation
Indices: 13877--14813 Score: 1003
Period size: 98 Copynumber: 9.6 Consensus size: 97
13867 AGGAGCAGAG
* * * * * *
13877 TAAAACAAGTAGCAGATCTCAATCTCCACTGGAGTTGCAATGGAACGAAGTGAAGCCACACCCAA
1 TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCA-CCAA
* * * *
13942 ATCCTATATCCCTGGAGATGTAATGGATCAGAT
65 ATCCTATATCCCTGAAGATGCAGTGGATCGGAT
* * * *
13975 TGAAACAAGTAGCAAATCTCAATCTCCACTGAAGTTGCAATGGAATGGAGTGAAGCCCCATCCAA
1 TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCA-CCAA
* * **
14040 ATCCTATATTCCTAAAGATGCAGTGGATCAAAT
65 ATCCTATATCCCTGAAGATGCAGTGGATCGGAT
* * * * * *
14073 TAAAACAAGTAACAGATTTCAATCTCTATTGAAGTTGTAGTGGAATGGAGTGAAGCCACATACAA
1 TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCA-CCAA
* *
14138 ATCCTATATCCCT-ATAGATACAGTGCATCGGAT
65 ATCCTATATCCCTGA-AGATGCAGTGGATCGGAT
* * * *
14171 TAAAACAAGTAGAAGATCTTAATCTCCACTGAAGTTGTAGTGGAATGGAATGATGCCACC-CCAA
1 TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCC-CCACCAA
* * *
14235 ACCCTATATCCCTGAAGATGCAGTCGATTGGAT
65 ATCCTATATCCCTGAAGATGCAGTGGATCGGAT
* * ** * *
14268 TAAAACAAGTAGAAGATCTCAATCTTCACTGAAGTTGTAGTACAATGGAGTAAAGCCAC-CCAAA
1 TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCACCAAA
* *
14332 TCCTATATCCCTAAAGATGCAATGGATCGGAT
66 TCCTATATCCCTGAAGATGCAGTGGATCGGAT
* *
14364 TAAAACAAGTAGCAGATCTCAATCTCCATTGAAGGTGTAGTGGAATGGAGTGAAGCCACC-CCAA
1 TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCC-CCACCAA
* * *
14428 ATCCTATATCCCTAAAGATACAGTGGATCGAAT
65 ATCCTATATCCCTGAAGATGCAGTGGATCGGAT
** *
14461 TAAAACAAGTAGCAGATCTCAATCTCCACTTGAAGTTACAGTGGAATGAAGTGAAGCCACC-CCA
1 TAAAACAAGTAGCAGATCTCAATCTCCAC-TGAAGTTGTAGTGGAATGGAGTGAAGCC-CCACCA
* * * *
14525 AATCCTATATCCTTGAAGTTGCA-AGGATTGGAT
64 AATCCTATATCCCTGAAGATGCAGTGGATCGGAT
* * * *
14558 TAAACTAACAA-TAGCAAATCTCAATCTCCATTGAAGTTGTAGTGGAATGGAGTGAATCCACACC
1 T-AA--AACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCACC
* * * **
14622 AAATCCTATATCCTTGAAGTTGCA-AGGATCAAAT
63 AAATCCTATATCCCTGAAGATGCAGTGGATCGGAT
** * * *
14656 TAAAAGTAACAA-TAATAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGAAGTAAAGCCACAC
1 T--AA--AACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCA-
* *
14720 CCAAAGCCTATATCCCTGAAGATGTAGTGGATCGGAT
61 CCAAATCCTATATCCCTGAAGATGCAGTGGATCGGAT
*
14757 TAAAGTA-ACAGTAGCAGATCTCAATATCCACTGAAGTTGTAGTGGAATGGAGTGAAG
1 TAAA--ACA-AGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAG
14814 TTACAAACCC
Statistics
Matches: 714, Mismatches: 109, Indels: 30
0.84 0.13 0.04
Matches are distributed among these distances:
96 83 0.12
97 153 0.21
98 326 0.46
99 76 0.11
100 68 0.10
101 8 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (97 bp):
TAAAACAAGTAGCAGATCTCAATCTCCACTGAAGTTGTAGTGGAATGGAGTGAAGCCCCACCAAA
TCCTATATCCCTGAAGATGCAGTGGATCGGAT
Found at i:14643 original size:47 final size:47
Alignment explanation
Indices: 14489--14645 Score: 136
Period size: 47 Copynumber: 3.3 Consensus size: 47
14479 TCAATCTCCA
* * * *
14489 CTTGAAGTTACAGTGGAATGAAGTGAAGCCACCCCAAATCCTATATC
1 CTTGAAGTTGCAGTGGAATGGAGTGAATCCACACCAAATCCTATATC
* * * * * * * * *
14536 CTTGAAGTTGCA-AGGATTGGATTAAACTAACAATAGCAAATCTCAATCTC
1 CTTGAAGTTGCAGTGGAATGGAGTGAA-T--CCACACCAAATC-CTATATC
*
14586 CATTGAAGTTGTAGTGGAATGGAGTGAATCCACACCAAATCCTATATC
1 C-TTGAAGTTGCAGTGGAATGGAGTGAATCCACACCAAATCCTATATC
14634 CTTGAAGTTGCA
1 CTTGAAGTTGCA
14646 AGGATCAAAT
Statistics
Matches: 80, Mismatches: 24, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
46 9 0.11
47 21 0.26
48 6 0.08
49 17 0.21
50 6 0.08
51 11 0.14
52 10 0.12
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (47 bp):
CTTGAAGTTGCAGTGGAATGGAGTGAATCCACACCAAATCCTATATC
Found at i:16399 original size:5 final size:5
Alignment explanation
Indices: 16389--16444 Score: 76
Period size: 5 Copynumber: 10.6 Consensus size: 5
16379 TCTCTATAAT
*
16389 TTTTA TTTTA TTTTA ATTTA GTTTTA TTTTA TTTTA TTTTA TTTCTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTT-TA -TTTTA
16442 TTT
1 TTT
16445 CGTACCTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
5 35 0.76
6 8 0.17
7 3 0.07
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:16414 original size:21 final size:20
Alignment explanation
Indices: 16389--16444 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 20
16379 TCTCTATAAT
16389 TTTTATTTTATTTTAATTTA
1 TTTTATTTTATTTTAATTTA
*
16409 GTTTTATTTTATTTTATTTTA
1 -TTTTATTTTATTTTAATTTA
16430 TTTCTATTTTTATTT
1 TTT-TA-TTTTATTT
16445 CGTACCTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 3 0.09
21 21 0.66
22 8 0.25
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTATTTTATTTTAATTTA
Found at i:16491 original size:17 final size:17
Alignment explanation
Indices: 16471--16504 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16461 TCGCACTTAC
16471 AATTTAGTCCTTTATTT
1 AATTTAGTCCTTTATTT
* *
16488 AATTTTGTCGTTTATTT
1 AATTTAGTCCTTTATTT
16505 TGATTTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (17 bp):
AATTTAGTCCTTTATTT
Found at i:16677 original size:21 final size:20
Alignment explanation
Indices: 16648--16686 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16638 TATGTTGTTA
*
16648 TTTTATGCCATTTTTTTTATT
1 TTTTATGCC-TTTTATTTATT
*
16669 TTTTTTGCCTTTTATTTA
1 TTTTATGCCTTTTATTTA
16687 ATTTGCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.13, C:0.10, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTATGCCTTTTATTTATT
Found at i:16690 original size:21 final size:21
Alignment explanation
Indices: 16648--16690 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16638 TATGTTGTTA
*
16648 TTTTATGCCATTTTTTTTATT
1 TTTTATGCCATTTTTTTAATT
*
16669 TTTTTTGCC-TTTTATTTAATT
1 TTTTATGCCATTTT-TTTAATT
16690 T
1 T
16691 GCATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTATGCCATTTTTTTAATT
Found at i:21886 original size:15 final size:15
Alignment explanation
Indices: 21866--21901 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
21856 TTTTTTTGTT
21866 GGTGTTGAGTGTTGG
1 GGTGTTGAGTGTTGG
* *
21881 GGTGTTGGGTTTTGG
1 GGTGTTGAGTGTTGG
21896 GGTGTT
1 GGTGTT
21902 AGGTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.00, G:0.53, T:0.44
Consensus pattern (15 bp):
GGTGTTGAGTGTTGG
Found at i:21906 original size:15 final size:15
Alignment explanation
Indices: 21877--21907 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21867 GTGTTGAGTG
*
21877 TTGGGGTGTTGGGTT
1 TTGGGGTGTTAGGTT
21892 TTGGGGTGTTAGGTT
1 TTGGGGTGTTAGGTT
21907 T
1 T
21908 ATTTTGTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (15 bp):
TTGGGGTGTTAGGTT
Found at i:24744 original size:30 final size:30
Alignment explanation
Indices: 24708--24767 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
24698 CTGAGTTTTT
24708 AATTACGGTCACACTAGTTTTCTTAGGTAC
1 AATTACGGTCACACTAGTTTTCTTAGGTAC
24738 AATTACGGTCACACTAGTTTTCTTAGGTAC
1 AATTACGGTCACACTAGTTTTCTTAGGTAC
24768 TACATAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (30 bp):
AATTACGGTCACACTAGTTTTCTTAGGTAC
Found at i:24854 original size:33 final size:33
Alignment explanation
Indices: 24816--24890 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
24806 TAGATCATCC
24816 CGACGTCTAGTAACTTCGAAATTTCTTTTTTCA
1 CGACGTCTAGTAACTTCGAAATTTCTTTTTTCA
*
24849 CGACGTCTAGTAACTTCGGAATTTCTTTTTTCA
1 CGACGTCTAGTAACTTCGAAATTTCTTTTTTCA
24882 CGACGTCTA
1 CGACGTCTA
24891 TCATCGGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (33 bp):
CGACGTCTAGTAACTTCGAAATTTCTTTTTTCA
Found at i:28531 original size:26 final size:26
Alignment explanation
Indices: 28502--28553 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28492 AGGGAAAGAA
28502 ATGAATTATTTTATTCCAAAACTAAG
1 ATGAATTATTTTATTCCAAAACTAAG
28528 ATGAATTATTTTATTCCAAAACTAAG
1 ATGAATTATTTTATTCCAAAACTAAG
28554 TGTTTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (26 bp):
ATGAATTATTTTATTCCAAAACTAAG
Found at i:34996 original size:2 final size:2
Alignment explanation
Indices: 34989--35028 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
34979 TTTATGCCAA
* * *
34989 AT AT AT AT GT AT AT AT AT AT AT AA AT AT AC 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
35029 TTGTCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Done.