Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005466.1 Kokia drynarioides strain JFW-HI SEQ_119513, 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: 8527
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:615 original size:30 final size:30
Alignment explanation
Indices: 490--911 Score: 218
Period size: 29 Copynumber: 14.4 Consensus size: 30
480 AATTATCTAT
* *
490 AAATTACATTTTT-ACCTCGAACTTTCC-A
1 AAATTACATTTTTGACCCCAAACTTTCCAA
* *
518 AAATT-CTATTTTTGA-CCCTAATTTTCCAA
1 AAATTAC-ATTTTTGACCCCAAACTTTCCAA
* *
547 AATTTACA-TTTT-ACCCCTAAACTTTAC-A
1 AAATTACATTTTTGACCCC-AAACTTTCCAA
* * *
575 AATTTCCATTTTTGACCCCAAATTTTCCAA
1 AAATTACATTTTTGACCCCAAACTTTCCAA
* *
605 AAAGTACATTTTT-ACACCTAAACTTTCC-A
1 AAATTACATTTTTGAC-CCCAAACTTTCCAA
* ***
634 AAATTCCATTTTTGACCATGAACTTTCCAA
1 AAATTACATTTTTGACCCCAAACTTTCCAA
* *
664 AAATTACA-TTTT-ACCCTCGAAC-CTCCAA
1 AAATTACATTTTTGACCC-CAAACTTTCCAA
* * * * * ** *
692 AAACTCCATTTTTAACCTCGATTTTTCTAA
1 AAATTACATTTTTGACCCCAAACTTTCCAA
*
722 ATATTACCA-TTTT-ACCCCTAAACTTTCC-A
1 AAATTA-CATTTTTGACCCC-AAACTTTCCAA
* * * *
751 AAATTCCATTTTTGACACCAAACTTTTCAT
1 AAATTACATTTTTGACCCCAAACTTTCCAA
*
781 AAATTACATTTAT-ACCCTCAAACCTTT--AA
1 AAATTACATTTTTGACCC-CAAA-CTTTCCAA
* * * ** *
810 AAATTCCATTTTTTACCCTAATTTTTCCGA
1 AAATTACATTTTTGACCCCAAACTTTCCAA
* *** *
840 AAATTATCGTTTTACCCCCCGAA-TTTCCAA
1 AAATTA-CATTTTTGACCCCAAACTTTCCAA
* *
870 AAATTCCATTTTTGACCCCGAACTTT-CAA
1 AAATTACATTTTTGACCCCAAACTTTCCAA
899 AAATTACCATTTT
1 AAATTA-CATTTT
912 ACCCTCGGAT
Statistics
Matches: 297, Mismatches: 68, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
27 2 0.01
28 54 0.18
29 121 0.41
30 105 0.35
31 15 0.05
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTTGACCCCAAACTTTCCAA
Found at i:641 original size:59 final size:59
Alignment explanation
Indices: 475--915 Score: 352
Period size: 59 Copynumber: 7.5 Consensus size: 59
465 CCCTAAAGGT
* * * * * *
475 CCCCAAATTATCTATAAATTACATTTTTACCTC-GAACTTTCCAAAATTCTATTTTTGA
1 CCCCAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA
* * * *
533 -CCCTAATTTTCCAAAATTTACA-TTTTACCCCTAAACTTTACAAATTTCCATTTTTGA
1 CCCCAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA
* *
590 CCCCAAATTTTCCAAAAAGTACATTTTTACACCTAAACTTTCCAAAATTCCATTTTTGA
1 CCCCAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA
*** * * * * *
649 CCATGAACTTTCCAAAAATTACA-TTTTA-CCCTCGAAC-CTCCAAAAACTCCATTTTTAA
1 CCCCAAATTTTCCAAAAATTACATTTTTACCCCT-AAACTTTCC-AAAATTCCATTTTTGA
* * * * *
707 CCTCGATTTTTCTAAATATTACCA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA
1 CCCCAAATTTTCCAAAAATTA-CATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA
* * * * *
766 CACCAAACTTTT-CATAAATTACATTTATA-CCCTCAAACCTTT-AAAAATTCCATTTTTTA
1 CCCCAAA-TTTTCCAAAAATTACATTTTTACCCCT-AAA-CTTTCCAAAATTCCATTTTTGA
* * * * **
825 CCCTAATTTTTCCGAAAATTATC-GTTTTACCCCCCGAA-TTTCCAAAAATTCCATTTTTGA
1 CCCCAAATTTTCCAAAAATTA-CATTTTTA-CCCCTAAACTTTCC-AAAATTCCATTTTTGA
* *
885 CCCCGAACTTT-CAAAAATTACCA-TTTTACCC
1 CCCCAAATTTTCCAAAAATTA-CATTTTTACCC
916 TCGGATGTCT
Statistics
Matches: 301, Mismatches: 63, Indels: 38
0.75 0.16 0.09
Matches are distributed among these distances:
56 8 0.03
57 44 0.15
58 72 0.24
59 134 0.45
60 40 0.13
61 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (59 bp):
CCCCAAATTTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTGA
Found at i:939 original size:118 final size:117
Alignment explanation
Indices: 509--932 Score: 387
Period size: 117 Copynumber: 3.6 Consensus size: 117
499 TTTTACCTCG
* * * * * * *
509 AACTTTCCAAAATTCTATTTTTGA-CCCTAATTTTCCAAAATTTACATTTTACCC-CTAAACTTT
1 AACTTTCCAAAATTCCATTTTTGACCCCGAACTTT-CAAAAATTACATTTTACCCTCGAACCTCT
* * * * * * * * *
572 ACAAATTTCCA-TTTTTGACCCCAAATTTTCCAAAAAGTA-CATTTTTACACCTA
65 A-AAAATTCCATTTTTTAACCTCAATTTTTCGAAATATTACCA-TTTTACCCCCA
** *
625 AACTTTCCAAAATTCCATTTTTGACCATGAACTTTCCAAAAATTACATTTTACCCTCGAACCTCC
1 AACTTTCCAAAATTCCATTTTTGACCCCGAACTTT-CAAAAATTACATTTTACCCTCGAACCTCT
* * * *
690 AAAAACTCCA-TTTTTAACCTCGATTTTTCTAAATATTACCATTTTACCCCTA
65 AAAAATTCCATTTTTTAACCTCAATTTTTCGAAATATTACCATTTTACCCCCA
* * * * *
742 AACTTTCCAAAATTCCATTTTTGACACCAAACTTTTCATAAATTACATTTATACCCTCAAACCTT
1 AACTTTCCAAAATTCCATTTTTGACCCCGAAC-TTTCAAAAATTACATTT-TACCCTCGAACCTC
* * * *
807 TAAAAATTCCATTTTTTACCCT-AATTTTTCCGAAA-ATTATCGTTTTACCCCCCG
64 TAAAAATTCCATTTTTTAACCTCAATTTTT-CGAAATATTACCATTTTA-CCCCCA
* **
861 AA-TTTCCAAAAATTCCATTTTTGACCCCGAACTTTCAAAAATTACCATTTTACCCTCGGATGTC
1 AACTTTCC-AAAATTCCATTTTTGACCCCGAACTTTCAAAAATTA-CATTTTACCCTCGAACCTC
925 TAAAAATT
64 TAAAAATT
933 TTATTTTCAA
Statistics
Matches: 254, Mismatches: 44, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
116 23 0.09
117 104 0.41
118 81 0.32
119 46 0.18
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (117 bp):
AACTTTCCAAAATTCCATTTTTGACCCCGAACTTTCAAAAATTACATTTTACCCTCGAACCTCTA
AAAATTCCATTTTTTAACCTCAATTTTTCGAAATATTACCATTTTACCCCCA
Found at i:955 original size:118 final size:116
Alignment explanation
Indices: 509--959 Score: 394
Period size: 118 Copynumber: 3.8 Consensus size: 116
499 TTTTACCTCG
* * * * * * *
509 AACTTTCCAAAATTCTATTTTTGA-CCCTAATTTTCCAAAATTTACATTTTACCC-CTAAACTTT
1 AACTTTCCAAAATTCCATTTTTGACCCCGAACTTT-CAAAAATTACATTTTACCCTCGAACCTCT
* * * * * * *
572 ACAAATTTCCATTTTTGACCCCAAATTTTCC-AAAAAGTA-CATTTTTACACCTA
65 A-AAAATTCCATTTTT-AACCCGAATTTTCCGAAATATTACCA-TTTTACCCCCA
** *
625 AACTTTCCAAAATTCCATTTTTGACCATGAACTTTCCAAAAATTACATTTTACCCTCGAACCTCC
1 AACTTTCCAAAATTCCATTTTTGACCCCGAACTTT-CAAAAATTACATTTTACCCTCGAACCTCT
* * * *
690 AAAAACTCCATTTTTAACCTCG-ATTTTTCTAAATATTACCATTTTACCCCTA
65 AAAAATTCCATTTTTAACC-CGAATTTTCCGAAATATTACCATTTTACCCCCA
* * * * *
742 AACTTTCCAAAATTCCATTTTTGACACCAAACTTTTCATAAATTACATTTATACCCTCAAACCTT
1 AACTTTCCAAAATTCCATTTTTGACCCCGAAC-TTTCAAAAATTACATTT-TACCCTCGAACCTC
* * * * *
807 TAAAAATTCCATTTTTTACCCTAATTTTTCCGAAA-ATTATCGTTTTACCCCCCG
64 TAAAAATTCCATTTTTAACCCGAA-TTTTCCGAAATATTACCATTTTA-CCCCCA
* **
861 AA-TTTCCAAAAATTCCATTTTTGACCCCGAACTTTCAAAAATTACCATTTTACCCTCGGATGTC
1 AACTTTCC-AAAATTCCATTTTTGACCCCGAACTTTCAAAAATTA-CATTTTACCCTCGAACCTC
** * *
925 TAAAAATTTTATTTTCAAACCCGAACTTTCCGAAA
64 TAAAAATTCCATTTT-TAACCCGAATTTTCCGAAA
960 GTTGACATTT
Statistics
Matches: 273, Mismatches: 49, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
116 32 0.12
117 96 0.35
118 98 0.36
119 47 0.17
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (116 bp):
AACTTTCCAAAATTCCATTTTTGACCCCGAACTTTCAAAAATTACATTTTACCCTCGAACCTCTA
AAAATTCCATTTTTAACCCGAATTTTCCGAAATATTACCATTTTACCCCCA
Found at i:3364 original size:103 final size:103
Alignment explanation
Indices: 3185--3391 Score: 378
Period size: 103 Copynumber: 2.0 Consensus size: 103
3175 AATACAATCC
*
3185 TACATTTAAAAATGTAGTTAAAAATTTATTCAAAAAAATGTAGTTAAAAAAGTAATCGGTATTCG
1 TACATTTAAAAATGTAGCTAAAAATTTATTCAAAAAAATGTAGTTAAAAAAGTAATCGGTATTCG
*
3250 ACCAATAGATATACATTTCGCCCCAATCACTTTTAGAA
66 ACCAATAGATATACATTTCGCCCCAATCACTTTCAGAA
* *
3288 TACATTTAAAATTGTAGCTAAAAATTTATTCAAAAGAATGTAGTTAAAAAAGTAATCGGTATTCG
1 TACATTTAAAAATGTAGCTAAAAATTTATTCAAAAAAATGTAGTTAAAAAAGTAATCGGTATTCG
3353 ACCAATAGATATACATTTCGCCCCAATCACTTTCAGAA
66 ACCAATAGATATACATTTCGCCCCAATCACTTTCAGAA
3391 T
1 T
3392 CTCCAAGAAC
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (103 bp):
TACATTTAAAAATGTAGCTAAAAATTTATTCAAAAAAATGTAGTTAAAAAAGTAATCGGTATTCG
ACCAATAGATATACATTTCGCCCCAATCACTTTCAGAA
Found at i:4357 original size:30 final size:31
Alignment explanation
Indices: 4304--4369 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
4294 TAGTAAATGT
* *
4304 AAAATTATATTTTAGCCTCTTAAAAATGATA
1 AAAATTAGATTTAAGCCTCTTAAAAATGATA
* *
4335 AAAATTAGATTTAATCCT-TTAAAAATTATA
1 AAAATTAGATTTAAGCCTCTTAAAAATGATA
4365 AAAAT
1 AAAAT
4370 ATAAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
AAAATTAGATTTAAGCCTCTTAAAAATGATA
Done.