Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002979.1 Kokia drynarioides strain JFW-HI SEQ_115463, 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, 786
Length: 1311
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Found at i:495 original size:29 final size:29
Alignment explanation
Indices: 451--875 Score: 372
Period size: 29 Copynumber: 14.8 Consensus size: 29
441 TAAAGGTCCT
*
451 TAAACTGTCCAAAAATTCCGTTTTTACCCC
1 TAAACT-TCCAAAAATTCCATTTTTACCCC
* *
481 TAAACTTCTAAAAATTCCATTTTTAACCTC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* * *
511 GAAACTTCCCAAAATCCCATTTTTA-CCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
*** *
539 TAAAACTTTTTAAAATTCCTTTTTTA-CCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* * *
568 TCGAACTTCCAAAAATCCCATTTTGACCCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
*
598 AAAACTTCCAAAAATTCC-TTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * *
626 TGAACTTCCAAAAATCCCATTTTAACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
*
655 AAAACTTCCAAAAATTCCATTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* *
684 TAAACTCCCAAAAATCCCATTTTT-----
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * *
708 T--A-TCCCAAAAATTCCATTTTGACCCT
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * *
734 AAAACTTCCGAAACTTCCA-TTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* *
762 TAAACTCCCAAAAATCCCATTTTTTACCCC
1 TAAACTTCCAAAAATTCCA-TTTTTACCCC
* *
792 AAAACTTCTAAAAATTCCATTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * *
821 CAAACATCCAAAAATTTCATTTTTAACCCC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* *
851 -AAATTTTCCCAAAATTACCATTTTT
1 TAAA-CTTCCAAAAATT-CCATTTTT
876 CCCTCGAGAA
Statistics
Matches: 316, Mismatches: 62, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.05
22 1 0.00
24 1 0.00
28 48 0.15
29 171 0.54
30 71 0.22
31 7 0.02
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTTACCCC
Found at i:777 original size:136 final size:137
Alignment explanation
Indices: 452--853 Score: 412
Period size: 137 Copynumber: 2.9 Consensus size: 137
442 AAAGGTCCTT
* * * * * *
452 AAACTGTCCAAAAATTCCGTTTTTACCCCTAAACTTCTAAAAATTCCATTTTTAACCTCGAAACT
1 AAACT-TCCAAAAATTCC-ATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCCAAAACT
* * ** * ** * ** *
517 TCCCAAAATCCCATTTTTACCCTAAAACTTTTTAAAATTCCTTTTTTACCCTCGAACTTCCAAAA
64 TCCAAAAATTCCATTTTTACCCCCAAAC-ATCCAAAAATCCCATTTT----T--AAC-CCCAAAA
582 ATCCCATTTTGACCCCA
121 ATCCCATTTTGACCCCA
* * *
599 AAACTTCCAAAAATTCCTTTTTACCCCTGAACTTCCAAAAATCCCA-TTTTAACCCCAAAACTTC
1 AAACTTCCAAAAATTCCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTC
* * * *
663 CAAAAATTCCATTTTTACCCCTAAAC-TCCCAAAAATCCCATTTTTTATCCCAAAAATTCCATTT
66 CAAAAATTCCATTTTTACCCCCAAACAT-CCAAAAATCCCATTTTTAACCCCAAAAATCCCATTT
*
727 TGACCCTA
130 TGACCCCA
* * *
735 AAACTTCCGAAACTTCCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTTACCCCAAAACTTC
1 AAACTTCCAAAAATTCCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTC
* **
800 TAAAAATTCCATTTTTACCCCCAAACATCCAAAAATTTCATTTTTAACCCCAAA
66 CAAAAATTCCATTTTTACCCCCAAACATCCAAAAATCCCATTTTTAACCCCAAA
854 TTTTCCCAAA
Statistics
Matches: 221, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
136 62 0.28
137 64 0.29
138 1 0.00
139 1 0.00
142 1 0.00
143 11 0.05
144 38 0.17
145 26 0.12
146 12 0.05
147 5 0.02
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (137 bp):
AAACTTCCAAAAATTCCATTTTACCCCTAAACTCCCAAAAATCCCATTTTTAACCCCAAAACTTC
CAAAAATTCCATTTTTACCCCCAAACATCCAAAAATCCCATTTTTAACCCCAAAAATCCCATTTT
GACCCCA
Found at i:786 original size:79 final size:79
Alignment explanation
Indices: 633--795 Score: 265
Period size: 78 Copynumber: 2.1 Consensus size: 79
623 CCCTGAACTT
633 CCAAAAATCCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTCCCAAAAA
1 CCAAAAATCCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTCCCAAAAA
*
698 TCCCATTTTTTATC
66 TCCCATTTTTTACC
* * * * *
712 CCAAAAATTCCATTTTGACCCTAAAACTTCCGAAACTTCCA-TTTTACCCCTAAACTCCCAAAAA
1 CCAAAAATCCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTCCCAAAAA
776 TCCCATTTTTTACC
66 TCCCATTTTTTACC
790 CCAAAA
1 CCAAAA
796 CTTCTAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 42 0.54
79 36 0.46
ACGTcount: A:0.36, C:0.33, G:0.01, T:0.29
Consensus pattern (79 bp):
CCAAAAATCCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTCCCAAAAA
TCCCATTTTTTACC
Found at i:824 original size:108 final size:107
Alignment explanation
Indices: 605--820 Score: 267
Period size: 108 Copynumber: 2.0 Consensus size: 107
595 CCCAAAACTT
* * *
605 CCAAAAATTCCTTTTTACCCCTGAACTTCCAAAAATCCCATTTTAACCCCAAAACTTCCAAAAAT
1 CCAAAAATTCCTTTTGACCCCTAAACTTCCAAAAATCCCATTTTAACCCCAAAACTCCCAAAAAT
* * *
670 TCCATTTTTACCCCTAAACTCCCAAAAATCCCATTTTTTATC
66 CCCATTTTTACCCCAAAACTCCCAAAAATCCCATTTTTTACC
* * * *
712 CCAAAAATTCCATTTTGA-CCCTAAAACTTCCGAAACTTCCATTTT-ACCCCTAAACTCCCAAAA
1 CCAAAAATTCC-TTTTGACCCCT-AAACTTCCAAAAATCCCATTTTAACCCCAAAACTCCCAAAA
* * *
775 ATCCCATTTTTTACCCCAAAACTTCTAAAAATTCCA-TTTTTACC
64 ATCCCA-TTTTTACCCCAAAACTCCCAAAAATCCCATTTTTTACC
819 CC
1 CC
821 CAAACATCCA
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
107 45 0.48
108 48 0.52
ACGTcount: A:0.34, C:0.33, G:0.01, T:0.31
Consensus pattern (107 bp):
CCAAAAATTCCTTTTGACCCCTAAACTTCCAAAAATCCCATTTTAACCCCAAAACTCCCAAAAAT
CCCATTTTTACCCCAAAACTCCCAAAAATCCCATTTTTTACC
Found at i:892 original size:59 final size:59
Alignment explanation
Indices: 712--875 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 59
702 ATTTTTTATC
* * * * * *
712 CCAAAAATTCCA-TTTTGACCCTAAAACTTCCGAAACTTCCA-TTTTACCCCTAAAC-T
1 CCAAAAATTTCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACAT
** * *
768 CCCAAAAATCCCATTTTTTACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCAAACAT
1 -CCAAAAATTTCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACAT
** *
828 CCAAAAATTTCATTTTTAACCCCAAATTTTCCCAAAATTACCATTTTT
1 CCAAAAATTTCATTTTTAACCCCAAAACTTCCAAAAATT-CCATTTTT
876 CCCTCGAGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
57 11 0.12
58 24 0.27
59 45 0.51
60 9 0.10
ACGTcount: A:0.35, C:0.30, G:0.01, T:0.33
Consensus pattern (59 bp):
CCAAAAATTTCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACAT
Done.