Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003127.1 Kokia drynarioides strain JFW-HI SEQ_115702, 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, 696
Length: 1161
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Found at i:616 original size:29 final size:31
Alignment explanation
Indices: 565--625 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
555 ACTCGAGGGA
* *
565 AAAATGGTAATTTTGGAAAATTTTAGGGTTT
1 AAAATGGTAATTTTAGAAAATTTGAGGGTTT
*
596 AAAATGG-AATTTTAG-ACATTTGAGGGTTT
1 AAAATGGTAATTTTAGAAAATTTGAGGGTTT
625 A
1 A
626 GTGTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
30 7 0.26
31 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (31 bp):
AAAATGGTAATTTTAGAAAATTTGAGGGTTT
Found at i:679 original size:29 final size:28
Alignment explanation
Indices: 646--810 Score: 80
Period size: 30 Copynumber: 5.6 Consensus size: 28
636 TTTAGGGTTT
646 AAATTCGAGGTAAAAAATGGATTTTTTGG
1 AAATTCGAGGT-AAAAATGGATTTTTTGG
* * * * *
675 AAATTTGAGGGTATAATTGTAATTTTTTAG
1 AAATTCGA-GGTAAAAATG-GATTTTTTGG
** * * *
705 AGTTTTGGGGTCAAAAATGGAGTTTTTGG
1 AAATTCGAGGT-AAAAATGGATTTTTTGG
* * * *
734 ACATTCGGGGGT-AAAATGTATTTTTTAG
1 AAATTC-GAGGTAAAAATGGATTTTTTGG
* * * *
762 AAGTCTAGGGGTCAAAAATGGAATTTTTGG
1 AAAT-TCGAGGT-AAAAATGGATTTTTTGG
*
792 AGATTCGAGGGTAAAAATG
1 AAATTCGA-GGTAAAAATG
811 TAATTTTTAG
Statistics
Matches: 99, Mismatches: 29, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
28 20 0.20
29 35 0.35
30 44 0.44
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
AAATTCGAGGTAAAAATGGATTTTTTGG
Found at i:732 original size:59 final size:60
Alignment explanation
Indices: 658--1027 Score: 363
Period size: 59 Copynumber: 6.3 Consensus size: 60
648 ATTCGAGGTA
* * * *
658 AAAAATGGATTTTTTGGAAATTTGAGGGTATAATTGTAATTTTTTAG-AGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTTGGGGTC
* * * * *
717 AAAAATGGAGTTTTTGGACATTCGGGGGT-AAAATGT-ATTTTTTAGAAGTCTAGGGGTC
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTTGGGGTC
* * *
775 AAAAATGGAATTTTTGGAGATTCGAGGGTAAAAATGTAA-TTTTTAGAAGTTTAGGGGTT
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTTGGGGTC
* * * * * *
834 ATAAA-GAAAATTCTTGGAAGTT-TAGGGGTAAAAATATAATTTTTT-GAAGTTTTGGGG-C
1 AAAAATG-GAATTTTTGGAAATTCGA-GGGTAAAAATGTAATTTTTTAGAAGTTTTGGGGTC
* *
892 TAAAAATGGAATTTTT-GAAAGTTCGAGGGTAAATATAG-AATTTTTGA-AAGTTTTGGGGTC
1 -AAAAATGGAATTTTTGGAAA-TTCGAGGGTAAAAAT-GTAATTTTTTAGAAGTTTTGGGGTC
* * * * *
952 -AAAATGGAATTTTTGGAAGTTCAAGGGTAAAAATAG-AA-TTTTTGGAAGTTTCGGAGTC
1 AAAAATGGAATTTTTGGAAATTCGAGGGTAAAAAT-GTAATTTTTTAGAAGTTTTGGGGTC
1010 AAAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
1028 CAGTTTAGGG
Statistics
Matches: 258, Mismatches: 37, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
57 13 0.05
58 88 0.34
59 148 0.57
60 9 0.03
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (60 bp):
AAAAATGGAATTTTTGGAAATTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTTGGGGTC
Found at i:745 original size:30 final size:28
Alignment explanation
Indices: 711--1027 Score: 163
Period size: 29 Copynumber: 10.8 Consensus size: 28
701 TTAGAGTTTT
*
711 GGGGTCAAAAATGGAGTTTTTGGACATTCG
1 GGGGT-AAAAATGGAATTTTTGGA-ATTCG
* * * * *
741 GGGGT-AAAATGTATTTTTTAGAAGTCTA
1 GGGGTAAAAATGGAATTTTTGGAATTC-G
769 GGGGTCAAAAATGGAATTTTTGGAGATTCG
1 GGGGT-AAAAATGGAATTTTTGGA-ATTCG
* * * *
799 AGGGTAAAAATGTAATTTTTAGAAGTTTAG
1 GGGGTAAAAATGGAATTTTTGGAA--TTCG
* * * * **
829 GGGTTATAAA-GAAAATTCTTGGAAGTTTA
1 GGGGTAAAAATG-GAATTTTTGGAA-TTCG
** * *
858 GGGGTAAAAATATAATTTTTTGAAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAA--TTCG
* *
888 GGGCTAAAAATGGAATTTTTGAAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAA-TTCG
* * * * **
917 AGGGTAAATATAGAATTTTTGAAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAA-TTCG
* *
946 GGGGTCAAAATGGAATTTTTGGAAGTTCA
1 GGGGTAAAAATGGAATTTTTGGAA-TTCG
* *
975 AGGGTAAAAATAGAATTTTTGGAAGTTTC-
1 GGGGTAAAAATGGAATTTTTGGAA--TTCG
*
1004 GGAGTCAAAAATGGAATTTTTGGA
1 GGGGT-AAAAATGGAATTTTTGGA
1028 CAGTTTAGGG
Statistics
Matches: 218, Mismatches: 58, Indels: 22
0.73 0.19 0.07
Matches are distributed among these distances:
27 3 0.01
28 20 0.09
29 108 0.50
30 84 0.39
31 3 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGGAATTCG
Found at i:815 original size:29 final size:28
Alignment explanation
Indices: 648--1027 Score: 158
Period size: 29 Copynumber: 13.0 Consensus size: 28
638 TAGGGTTTAA
* * *
648 ATTCGAGGTAAAAAATGGATTTTTTGGAA
1 ATTCGGGGT-AAAAATGGAATTTTTGGAG
* * * * *
677 ATTTGAGGGTATAATTGTAATTTTTTAGAG
1 ATTCG-GGGTAAAAATGGAA-TTTTTGGAG
* * * *
707 TTTTGGGGTCAAAAATGGAGTTTTTGGAC
1 ATTCGGGGT-AAAAATGGAATTTTTGGAG
* * *
736 ATTCGGGGGT-AAAATGTATTTTTTAGA-
1 ATTC-GGGGTAAAAATGGAATTTTTGGAG
*
763 AGTCTAGGGGTCAAAAATGGAATTTTTGGAG
1 A-T-TCGGGGT-AAAAATGGAATTTTTGGAG
* *
794 ATTCGAGGGTAAAAATGTAATTTTTAGAAG
1 ATTCG-GGGTAAAAATGGAATTTTT-GGAG
* * * * *
824 TTTAGGGGTTATAAA-GAAAATTCTTGGAAG
1 ATTCGGGG-TAAAAATG-GAATTTTTGG-AG
* * ** *
854 TTTAGGGGTAAAAATATAATTTTTTGAAG
1 ATTCGGGGTAAAAATGGAA-TTTTTGGAG
* * *
883 TTTTGGGGCTAAAAATGGAATTTTT-GAA
1 ATTCGGGG-TAAAAATGGAATTTTTGGAG
* * *
911 AGTTCGAGGGTAAATATAGAATTTTTGAAAG
1 A-TTCG-GGGTAAAAATGGAATTTTTG-GAG
* * *
942 TTTTGGGGTCAAAATGGAATTTTTGGA-
1 ATTCGGGGTAAAAATGGAATTTTTGGAG
* *
969 AGTTCAAGGGTAAAAATAGAATTTTTGGAAG
1 A-TTC-GGGGTAAAAATGGAATTTTTGG-AG
* *
1000 TTTCGGAGTCAAAAATGGAATTTTTGGA
1 ATTCGGGGT-AAAAATGGAATTTTTGGA
1028 CAGTTTAGGG
Statistics
Matches: 261, Mismatches: 64, Indels: 52
0.69 0.17 0.14
Matches are distributed among these distances:
27 1 0.00
28 24 0.09
29 123 0.47
30 111 0.43
31 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
ATTCGGGGTAAAAATGGAATTTTTGGAG
Done.