Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006717.1 Kokia drynarioides strain JFW-HI SEQ_121313, 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: 4359
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Found at i:520 original size:29 final size:29
Alignment explanation
Indices: 457--844 Score: 220
Period size: 29 Copynumber: 13.5 Consensus size: 29
447 TTAACTTTCT
* * **
457 AAAATTACATTTTTGACTTCAAACCTTCCCA
1 AAAATCACATTTTTGCCCCCAAA-CTT-CCA
* *
488 AAATTC-CATTTTTGCCCCCAAACTTTCA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
* * **
516 AAAATCATATTTTTACCCTTAAACTTCCA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
* * **
545 AAAATTACA-TTTTG-ACATAAACTTTCC-
1 AAAATCACATTTTTGCCCCCAAAC-TTCCA
* **** * *
572 AAAATTACATTTTTTGACCTTGGACCTTCTTA
1 AAAATCACA-TTTTTG-CCCCCAAACTTC-CA
* *
604 AAATTC-CA-TTTTACCCCCAAACTTCCA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
* *
631 AAAATCATATTTTT-CCCCCAAACTTCTA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
* * * *
659 AAAATCATATTTTTACCCCTAAACTTCAA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
* * *
688 AAAATCACATTTTTACCCTCGAACTTCCA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
**
717 AAAATCACATTTTT-CCCCTGAACTTCCA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
*
745 AAAATCACA-TTTTGTCCCCGAAA-TTCCA
1 AAAATCACATTTTTG-CCCCCAAACTTCCA
* * **
773 AAAATCACATTTTTACCCTCGGACTTCCA
1 AAAATCACATTTTTGCCCCCAAACTTCCA
* * * * ** *
802 AAGATCACGTTTTTACCCCGAATTTTCCT
1 AAAATCACATTTTTGCCCCCAAACTTCCA
*
831 AAAATAACATTTTT
1 AAAATCACATTTTT
845 ATCCCTAAAA
Statistics
Matches: 278, Mismatches: 64, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
27 25 0.09
28 89 0.32
29 136 0.49
30 16 0.06
31 8 0.03
32 4 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATCACATTTTTGCCCCCAAACTTCCA
Found at i:579 original size:115 final size:114
Alignment explanation
Indices: 449--785 Score: 312
Period size: 114 Copynumber: 2.9 Consensus size: 114
439 TTCATCTCTT
* *
449 AACTTTCTAAAATTACA-TTTTTGA-CTTCAAACCTTCCCAAAATTCCATTTTTGCCCCCAAACT
1 AACTTTCCAAAATTACATTTTTTGACCTT-AAACCTTCCCAAAATTCCA-TTTTACCCCCAAACT
* **
512 TTCAAAAATCATATTTTTACCCTTAAACTTCCAAAAATTACATTTTGACATA
64 TCCAAAAATCATATTTTT-CCCCCAAACTTCCAAAAATTACATTTTGACATA
** **
564 AACTTTCCAAAATTACATTTTTTGACCTTGGACCTTCTTAAAATTCCATTTTACCCCCAAACTTC
1 AACTTTCCAAAATTACATTTTTTGACCTTAAACCTTCCCAAAATTCCATTTTACCCCCAAACTTC
* * * * *
629 CAAAAATCATATTTTTCCCCCAAACTTCTAAAAATCATATTTTTACCCCTA
66 CAAAAATCATATTTTTCCCCCAAACTTCCAAAAATTACATTTTGA--CATA
* * ** * * **
680 AAC-TTCAAAAAATCACA-TTTTT-ACCCTCGAA-CTT-CCAAAAATCACATTTTTCCCCTGAAC
1 AACTTTC-CAAAATTACATTTTTTGA-CCTTAAACCTTCCCAAAATTC-CATTTTACCCCCAAAC
* * *
740 TTCCAAAAATCACATTTTGTCCCCGAAA-TTCCAAAAATCACATTTT
63 TTCCAAAAATCATATTTT-TCCCCCAAACTTCCAAAAATTACATTTT
786 TACCCTCGGA
Statistics
Matches: 186, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
113 6 0.03
114 73 0.39
115 68 0.37
116 36 0.19
117 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (114 bp):
AACTTTCCAAAATTACATTTTTTGACCTTAAACCTTCCCAAAATTCCATTTTACCCCCAAACTTC
CAAAAATCATATTTTTCCCCCAAACTTCCAAAAATTACATTTTGACATA
Found at i:644 original size:58 final size:57
Alignment explanation
Indices: 481--819 Score: 212
Period size: 57 Copynumber: 5.9 Consensus size: 57
471 GACTTCAAAC
* * *
481 CTTCCCAAAATTCCATTTTTGCCCCCAAACTTTCAAAAATCATATTTTTACCCTTAAA
1 CTTCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCATATTTTTACCCTTAAA
* ** * * *
539 CTTCCAAAAATTACATTTTGA--CATAAACTTTCCAAAATTACAT-TTTTTGA-CCTTGGAC
1 CTTCCAAAAATTCCATTTT-ACCCCCAAAC-TTCCAAAAAT-CATATTTTT-ACCCTT-AAA
** **
597 CTTCTTAAAATTCCATTTTACCCCCAAACTTCCAAAAATCATATTTTT-CCCCCAAA
1 CTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAATCATATTTTTACCCTTAAA
* * * * * **
653 CTTCTAAAAA-TCATATTTTTACCCCTAAACTTCAAAAAATCACATTTTTACCCTCGAA
1 CTTCCAAAAATTC-CA-TTTTACCCCCAAACTTCCAAAAATCATATTTTTACCCTTAAA
* ** * **
711 CTTCCAAAAA-TCACATTTTTCCCCTGAACTTCCAAAAATCACATTTTGT-CCCCGAAA
1 CTTCCAAAAATTC-CATTTTACCCCCAAACTTCCAAAAATCATATTTT-TACCCTTAAA
* ** * **
768 -TTCCAAAAA-TCACATTTTTACCCTCGGACTTCCAAAGATCACGTTTTTACCC
1 CTTCCAAAAATTC-CA-TTTTACCCCCAAACTTCCAAAAATCATATTTTTACCC
820 CGAATTTTCC
Statistics
Matches: 226, Mismatches: 40, Indels: 31
0.76 0.13 0.10
Matches are distributed among these distances:
55 2 0.01
56 31 0.14
57 120 0.53
58 68 0.30
59 5 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (57 bp):
CTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAATCATATTTTTACCCTTAAA
Found at i:691 original size:57 final size:57
Alignment explanation
Indices: 612--853 Score: 256
Period size: 57 Copynumber: 4.2 Consensus size: 57
602 TAAAATTCCA
* * * *
612 TTTTACCCCCAAACTTCCAAAAATCATATTTTTCCCCCAAACTTCTAAAAATCATAT
1 TTTTACCCCTAAACTTCCAAAAATCACATTTTTCCCCCAAACTTCCAAAAATCACAT
* * *
669 TTTTACCCCTAAACTTCAAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACAT
1 TTTTACCCCTAAACTTCCAAAAATCACATTTTT-CCCCCAAACTTCCAAAAATCACAT
* *
727 TTTT-CCCCTGAACTTCCAAAAATCACATTTTGTCCCCGAAA-TTCCAAAAATCACAT
1 TTTTACCCCTAAACTTCCAAAAATCACATTTT-TCCCCCAAACTTCCAAAAATCACAT
** * * * ** * *
783 TTTTA-CCCTCGGACTTCCAAAGATCACGTTTTTACCCCGAATTTTCCTAAAATAACAT
1 TTTTACCCCT-AAACTTCCAAAAATCACATTTTT-CCCCCAAACTTCCAAAAATCACAT
*
841 TTTTATCCCTAAA
1 TTTTACCCCTAAA
854 ACTTTTCAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
56 24 0.15
57 86 0.54
58 44 0.28
59 4 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
TTTTACCCCTAAACTTCCAAAAATCACATTTTTCCCCCAAACTTCCAAAAATCACAT
Found at i:728 original size:114 final size:112
Alignment explanation
Indices: 497--843 Score: 315
Period size: 114 Copynumber: 3.0 Consensus size: 112
487 AAAATTCCAT
* * ** * *
497 TTTTGCCCCCAAACTTTCAAAAATCATATTTTTACCCTTAAACTTCCAAAAATTACATTTTGA-C
1 TTTTACCCCCAAACTTCCAAAAATCATATTTTT-CCCCCAAACTTCCAAAAATCACATTTTTACC
* * * * * * * *
561 ATAAACTTTCCAAAATTACATTTTTTGACCTTGGACCTTCTTAAAATTC-CA
65 CTAAAC-TTCAAAAATCACA-TTTTT-ACCCTCGAACTTC-CAAAAATCACA
* *
612 TTTTACCCCCAAACTTCCAAAAATCATATTTTTCCCCCAAACTTCTAAAAATCATATTTTTACCC
1 TTTTACCCCCAAACTTCCAAAAATCATATTTTTCCCCCAAACTTCCAAAAATCACATTTTTA-CC
677 CTAAACTTCAAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACA
65 CTAAACTTC-AAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACA
* ** * *
726 TTTTTCCCCTGAACTTCCAAAAATCACATTTTGTCCCCGAAA-TTCCAAAAATCACATTTTTACC
1 TTTTACCCCCAAACTTCCAAAAATCATATTTT-TCCCCCAAACTTCCAAAAATCACATTTTTACC
** * * * * *
790 CTCGGACTTCCAAAGATCACGTTTTTACCC-CGAATTTTCCTAAAATAACA
65 CT-AAACTT-CAAAAATCACATTTTTACCCTCGAA-CTTCCAAAAATCACA
840 TTTT
1 TTTT
844 TATCCCTAAA
Statistics
Matches: 194, Mismatches: 30, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
113 14 0.07
114 118 0.61
115 48 0.25
116 14 0.07
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (112 bp):
TTTTACCCCCAAACTTCCAAAAATCATATTTTTCCCCCAAACTTCCAAAAATCACATTTTTACCC
TAAACTTCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATCACA
Found at i:845 original size:29 final size:28
Alignment explanation
Indices: 612--845 Score: 256
Period size: 29 Copynumber: 8.2 Consensus size: 28
602 TAAAATTCCA
* *
612 TTTTACCCCCAAACTTCCAAAAATCATAT
1 TTTTA-CCCCGAACTTCCAAAAATCACAT
* * * *
641 TTTTCCCCCAAACTTCTAAAAATCATAT
1 TTTTACCCCGAACTTCCAAAAATCACAT
* *
669 TTTTACCCCTAAACTTCAAAAAATCACAT
1 TTTTACCCC-GAACTTCCAAAAATCACAT
698 TTTTACCCTCGAACTTCCAAAAATCACAT
1 TTTTACCC-CGAACTTCCAAAAATCACAT
727 TTTT-CCCCTGAACTTCCAAAAATCACAT
1 TTTTACCCC-GAACTTCCAAAAATCACAT
*
755 TTTGT-CCCCGAAATTCCAAAAATCACAT
1 TTT-TACCCCGAACTTCCAAAAATCACAT
* * *
783 TTTTACCCTCGGACTTCCAAAGATCACGT
1 TTTTACCC-CGAACTTCCAAAAATCACAT
* * *
812 TTTTACCCCGAATTTTCCTAAAATAACAT
1 TTTTACCCCGAA-CTTCCAAAAATCACAT
841 TTTTA
1 TTTTA
846 TCCCTAAAAC
Statistics
Matches: 180, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
27 2 0.01
28 82 0.46
29 95 0.53
30 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATCACAT
Done.