Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004980.1 Kokia drynarioides strain JFW-HI SEQ_118721, 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, 934
Length: 1558
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Found at i:387 original size:30 final size:29
Alignment explanation
Indices: 353--597 Score: 97
Period size: 29 Copynumber: 8.4 Consensus size: 29
343 GTCCCTAATT
*
353 TTTCCAAAAATCACGATTTGTCCCCCAAAC
1 TTTCCAAAAATCAC-ATTTGGCCCCCAAAC
* *
383 TTTCCAAAAATTACAATTTGGCTCCCAAAC
1 TTTCCAAAAATCAC-ATTTGGCCCCCAAAC
* * * * *
413 ATT-AAAAAATCACATTTTGACCCTCGAAC
1 TTTCCAAAAATCACA-TTTGGCCCCCAAAC
* ** * *
442 -TTCACAAAAATTACATTTTACCCTCAAGC
1 TTTC-CAAAAATCACATTTGGCCCCCAAAC
* * * ** ***
471 -TTCACACAAATTATATTTTTACCCTTGAAC
1 TTTC-CAAAAATCACA-TTTGGCCCCCAAAC
* ** *
501 TTTCCAAAAATTACATTTTACCCCTAAAC
1 TTTCCAAAAATCACATTTGGCCCCCAAAC
*
530 -TTCCAAAAATCACATTTTTGCCCCCAAAC
1 TTTCCAAAAATCACA-TTTGGCCCCCAAAC
* * ** *
559 -TTCAAAAAATTATCATTTTACCCCCGAAC
1 TTTCCAAAAATCA-CATTTGGCCCCCAAAC
588 -TTCCAAAAAT
1 TTTCCAAAAAT
598 ATCATTCTTG
Statistics
Matches: 175, Mismatches: 33, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
28 16 0.09
29 97 0.55
30 59 0.34
31 3 0.02
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTCCAAAAATCACATTTGGCCCCCAAAC
Found at i:450 original size:29 final size:28
Alignment explanation
Indices: 417--866 Score: 233
Period size: 29 Copynumber: 15.5 Consensus size: 28
407 CCAAACATTA
*
417 AAAAATCACATTTTGACCCTCGAACTTCAC
1 AAAAATTACATTTT-ACCCTCGAACTTC-C
447 AAAAATTACATTTTACCCTC-AAGCTTCAC
1 AAAAATTACATTTTACCCTCGAA-CTTC-C
* * *
476 ACAAATTATATTTTTACCCTTGAACTTTCC
1 AAAAATTACA-TTTTACCCTCGAAC-TTCC
*
506 AAAAATTACATTTTACCC-CTAAACTTCC
1 AAAAATTACATTTTACCCTC-GAACTTCC
* * * * *
534 AAAAATCACATTTTTGCCCCCAAACTTCA
1 AAAAATTACA-TTTTACCCTCGAACTTCC
*
563 AAAAATTATCATTTTACCCCCGAACTTCC
1 AAAAATTA-CATTTTACCCTCGAACTTCC
* **
592 AAAAA-TATCATTCTTGA-CC-CGAAGTTTTT
1 AAAAATTA-CATT-TT-ACCCTCGAA-CTTCC
* * * * *
621 GAAAATTACTGTTTTACACTCGAATTTCA
1 AAAAATTAC-ATTTTACCCTCGAACTTCC
* *
650 AAAAATTACCATTTTA-CCTCTTAATTTCC
1 AAAAATTA-CATTTTACCCTC-GAACTTCC
* *
679 AAAAATTCCATTTTTAACCC-CGAACTTGCA
1 AAAAATTACA-TTTT-ACCCTCGAACTT-CC
*
709 AAAAATTACCATTTTACCCT-TAGA-TGTCC
1 AAAAATTA-CATTTTACCCTCGA-ACT-TCC
* * ** *
738 -AAAATTCCATTTTTAACCTTAAACTTTCA
1 AAAAATTACA-TTTTACCCTCGAAC-TTCC
*
767 AAAAATTACATTTTACCC-CTGAACTACC
1 AAAAATTACATTTTACCCTC-GAACTTCC
* * *
795 AAAAAATCACATTTTTGCCCTCAAACTTCC
1 -AAAAATTACA-TTTTACCCTCGAACTTCC
* *
825 -AAAATTACCATTTTTCCCCCGAACTTCC
1 AAAAATTA-CATTTTACCCTCGAACTTCC
853 AAAAA-TATCATTTT
1 AAAAATTA-CATTTT
867 TAACCCTAAA
Statistics
Matches: 330, Mismatches: 54, Indels: 74
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.01
28 78 0.24
29 157 0.48
30 83 0.25
31 10 0.03
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAAATTACATTTTACCCTCGAACTTCC
Found at i:489 original size:59 final size:58
Alignment explanation
Indices: 417--611 Score: 202
Period size: 59 Copynumber: 3.3 Consensus size: 58
407 CCAAACATTA
*
417 AAAAATCACATTTTGACCCTCGAACTTCACAAAAATTACATTTTA-CCCTCAAGCTTCAC
1 AAAAATCACATTTTGACCCTCGAACTTCACAAAAATTACATTTTACCCCT-AAACTTC-C
* * * * *
476 ACAAATTATATTTTTACCCTTGAACTTTC-CAAAAATTACATTTTACCCCTAAACTTCC
1 AAAAATCACATTTTGACCCTCGAAC-TTCACAAAAATTACATTTTACCCCTAAACTTCC
* * **
534 AAAAATCACATTTTTG-CCCCCAAACTTCA-AAAAATTATCATTTTACCCCCGAACTTCC
1 AAAAATCACA-TTTTGACCCTCGAACTTCACAAAAATTA-CATTTTACCCCTAAACTTCC
592 AAAAAT-ATCATTCTTGACCC
1 AAAAATCA-CATT-TTGACCC
612 GAAGTTTTTG
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
57 14 0.12
58 43 0.38
59 49 0.43
60 7 0.06
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAAATCACATTTTGACCCTCGAACTTCACAAAAATTACATTTTACCCCTAAACTTCC
Found at i:546 original size:87 final size:87
Alignment explanation
Indices: 417--926 Score: 304
Period size: 87 Copynumber: 5.8 Consensus size: 87
407 CCAAACATTA
* * *
417 AAAAATCACATTTTGA-CCCTCGAACTTCACAAAAATTACATTTTACCCTCAAGCTTCACACAAA
1 AAAAATTACATTTTGACCCCT-AAACTTC-CAAAAATTACATTTTACCCTCAAACTTCACA-AAA
*
481 TTATATTTTTACCCTTGAACTTTCC
63 TTACATTTTTACCCTTGAACTTTCC
* * * *
506 AAAAATTACATTTT-ACCCCTAAACTTCCAAAAATCACATTTTTGCCCCCAAACTTCAAAAAATT
1 AAAAATTACATTTTGACCCCTAAACTTCCAAAAATTACA-TTTTACCCTCAAACTTCACAAAATT
**
570 ATCA-TTTTACCCCCGAAC-TTCC
65 A-CATTTTTACCCTTGAACTTTCC
* ** *** * * * * *
592 AAAAA-TATCATTCTTGA-CCCGAAGTTTTTGAAAATTACTGTTTTACACTCGAATTTCAAAAAA
1 AAAAATTA-CATT-TTGACCCCTAAACTTCCAAAAATTAC-ATTTTACCCTCAAACTTCACAAAA
655 TTACCA-TTTTACCTCTT-AA-TTTCC
63 TTA-CATTTTTACC-CTTGAACTTTCC
* * * * * *
679 AAAAATTCCATTTTTAACCCC-GAACTTGCAAAAAATTACCATTTTACCCTTAGA-TGTC-CAAA
1 AAAAATTACA-TTTTGACCCCTAAACTT-CCAAAAATTA-CATTTTACCCTCAAACT-TCACAAA
* * * *
741 ATTCCATTTTTAACCTTAAACTTTCA
62 ATTACATTTTTACCCTTGAACTTTCC
* * * *
767 AAAAATTACATTTT-ACCCCTGAACTACCAAAAAATCACATTTTTGCCCTCAAACTTC-CAAAAT
1 AAAAATTACATTTTGACCCCTAAACTTCC-AAAAATTACA-TTTTACCCTCAAACTTCACAAAAT
**
830 TACCATTTTT-CCCCCGAAC-TTCC
64 TA-CATTTTTACCCTTGAACTTTCC
* * **
853 AAAAA-TATCATTTTTAACCCTAAA-TTCTTTAAAATTACCATTTTACCC-CTAAACTTC-CAAA
1 AAAAATTA-CATTTTGACCCCTAAACTTC-CAAAAATTA-CATTTTACCCTC-AAACTTCACAAA
*
914 AATATCATTTTTA
62 ATTA-CATTTTTA
927 ACCCCAAATT
Statistics
Matches: 327, Mismatches: 65, Indels: 60
0.72 0.14 0.13
Matches are distributed among these distances:
85 5 0.02
86 76 0.23
87 157 0.48
88 71 0.22
89 18 0.06
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (87 bp):
AAAAATTACATTTTGACCCCTAAACTTCCAAAAATTACATTTTACCCTCAAACTTCACAAAATTA
CATTTTTACCCTTGAACTTTCC
Found at i:628 original size:58 final size:57
Alignment explanation
Indices: 354--611 Score: 186
Period size: 59 Copynumber: 4.4 Consensus size: 57
344 TCCCTAATTT
* * ** *
354 TTCCAAAAATCACGA-T-TTGTCCCCCAAACTTTCCAAAAATTACAATTTGGCTCCCAAAC
1 TTCCAAAAATCAC-ATTCTTG-ACCCCAAAC-TTCAAAAAATTAC-ATTTTACCCCCAAAC
* * * *
413 ATT-AAAAAATCACATT-TTGACCCTCGAACTTCACAAAAATTACATTTTACCCTCAAGC
1 -TTCCAAAAATCACATTCTTGACCC-CAAACTTCA-AAAAATTACATTTTACCCCCAAAC
* * * * ** * *
471 TTCACACAAATTATATT-TTTACCCTTGAACTTTCCAAAAATTACATTTTACCCCTAAAC
1 TTC-CAAAAATCACATTCTTGACCC-CAAAC-TTCAAAAAATTACATTTTACCCCCAAAC
* * *
530 TTCCAAAAATCACATTTTTGCCCCCAAACTTCAAAAAATTATCATTTTACCCCCGAAC
1 TTCCAAAAATCACATTCTTGACCCCAAACTTCAAAAAATTA-CATTTTACCCCCAAAC
588 TTCCAAAAAT-ATCATTCTTGACCC
1 TTCCAAAAATCA-CATTCTTGACCC
612 GAAGTTTTTG
Statistics
Matches: 158, Mismatches: 31, Indels: 20
0.76 0.15 0.10
Matches are distributed among these distances:
57 14 0.09
58 64 0.41
59 75 0.47
60 5 0.03
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (57 bp):
TTCCAAAAATCACATTCTTGACCCCAAACTTCAAAAAATTACATTTTACCCCCAAAC
Found at i:722 original size:59 final size:58
Alignment explanation
Indices: 646--960 Score: 297
Period size: 58 Copynumber: 5.4 Consensus size: 58
636 ACACTCGAAT
* * * *
646 TTCAAAAAATTACCATTTTACCTCTTAATTTCCAAAAATTCCATTTTTAACCCCGAAC
1 TTCAAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAC
* **
704 TTGCAAAAAATTACCATTTTA-CCCTTAGA-TGTCC-AAAATTCCATTTTTAACCTTAAAC
1 TT-CAAAAAATTACCATTTTACCCCTGA-ACT-TCCAAAAATTCCATTTTTAACCCCAAAC
* * *
762 TTTCAAAAAATTA-CATTTTACCCCTGAACTACCAAAAAATCACATTTTT-GCCCTCAAAC
1 -TTCAAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTC-CATTTTTAACCC-CAAAC
* * * *
821 TTC-CAAAATTACCATTTTTCCCCCGAACTTCCAAAAATAT-CATTTTTAACCCTAAA-
1 TTCAAAAAATTACCATTTTACCCCTGAACTTCCAAAAAT-TCCATTTTTAACCCCAAAC
** * *
877 TTCTTTAAAATTACCATTTTACCCCTAAACTTCCAAAAATAT-CATTTTTAACCCCAAAT
1 TTC-AAAAAATTACCATTTTACCCCTGAACTTCCAAAAAT-TCCATTTTTAACCCCAAAC
* *
936 TATCTAAAAATTATCATTTTACCCC
1 T-TCAAAAAATTACCATTTTACCCC
961 AAAGCTTCTA
Statistics
Matches: 217, Mismatches: 24, Indels: 31
0.80 0.09 0.11
Matches are distributed among these distances:
56 3 0.01
57 27 0.12
58 129 0.59
59 56 0.26
60 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (58 bp):
TTCAAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAC
Found at i:867 original size:29 final size:29
Alignment explanation
Indices: 417--960 Score: 152
Period size: 29 Copynumber: 18.7 Consensus size: 29
407 CCAAACATTA
* *
417 AAAAATCA-CATTTTGACCCTCGAACTTCAC
1 AAAAAT-ATCATTTTTACCCCCGAACTTC-C
*
447 AAAAAT-TACA-TTTTACCCTC-AAGCTTCAC
1 AAAAATAT-CATTTTTACCCCCGAA-CTTC-C
* **
476 ACAAATTAT-ATTTTTACCCTTGAACTTTCC
1 A-AAAATATCATTTTTACCCCCGAAC-TTCC
**
506 AAAAAT-TACA-TTTTACCCCTAAACTTCC
1 AAAAATAT-CATTTTTACCCCCGAACTTCC
* * *
534 AAAAATCA-CATTTTTGCCCCCAAACTTCA
1 AAAAAT-ATCATTTTTACCCCCGAACTTCC
563 AAAAATTATCA-TTTTACCCCCGAACTTCC
1 AAAAA-TATCATTTTTACCCCCGAACTTCC
* * **
592 AAAAATATCATTCTTGA--CCCGAAGTTTTT
1 AAAAATATCATT-TTTACCCCCGAA-CTTCC
* * * * *
621 GAAAAT-T-ACTGTTTTACACTCGAATTTCA
1 AAAAATATCA-T-TTTTACCCCCGAACTTCC
* * ** *
650 AAAAATTACCA-TTTTACCTCTTAATTTCC
1 AAAAA-TATCATTTTTACCCCCGAACTTCC
* *
679 AAAAAT-TCCATTTTTAACCCCGAACTTGCA
1 AAAAATAT-CATTTTTACCCCCGAACTT-CC
* **
709 AAAAATTACCA-TTTTA-CCCTTAGA-TGTCC
1 AAAAA-TATCATTTTTACCCCCGA-ACT-TCC
* *** *
738 -AAAAT-TCCATTTTTAACCTTAAACTTTC
1 AAAAATAT-CATTTTTACCCCCGAACTTCC
* *
766 AAAAA-ATTACA-TTTTACCCCTGAACTACC
1 AAAAATA-T-CATTTTTACCCCCGAACTTCC
* * *
795 AAAAA-ATCACATTTTTGCCCTCAAACTTCC
1 AAAAATAT--CATTTTTACCCCCGAACTTCC
* *
825 AAAATTACCATTTTT-CCCCCGAACTTCC
1 AAAAATATCATTTTTACCCCCGAACTTCC
* * * *
853 AAAAATATCATTTTTA-ACCCTAAATTCTTT
1 AAAAATATCATTTTTACCCCCGAACTTC--C
* * **
883 AAAATTACCA-TTTTACCCCTAAACTTCC
1 AAAAATATCATTTTTACCCCCGAACTTCC
* * * *
911 AAAAATATCATTTTTAACCCCAAATTATCT
1 AAAAATATCATTTTTACCCCCGAACT-TCC
941 AAAAATTATCA-TTTTACCCC
1 AAAAA-TATCATTTTTACCCC
961 AAAGCTTCTA
Statistics
Matches: 386, Mismatches: 79, Indels: 98
0.69 0.14 0.17
Matches are distributed among these distances:
27 4 0.01
28 87 0.23
29 179 0.46
30 100 0.26
31 15 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATATCATTTTTACCCCCGAACTTCC
Found at i:1090 original size:29 final size:29
Alignment explanation
Indices: 1030--1091 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1020 CAAAGTGTCT
* * * * *
1030 AAAATTACCATTTTACCCTCTAACCTCTA
1 AAAAGTACCACTTTACCCTCGAACATCCA
*
1059 AAAAGTACCACTTTACCCTCGAGCATCCA
1 AAAAGTACCACTTTACCCTCGAACATCCA
1088 AAAA
1 AAAA
1092 TCGTATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.31, G:0.05, T:0.26
Consensus pattern (29 bp):
AAAAGTACCACTTTACCCTCGAACATCCA
Done.