Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009929.1 Kokia drynarioides strain JFW-HI SEQ_124670, 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: 2872
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.29
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:639 original size:12 final size:12
Alignment explanation
Indices: 622--647 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
612 AAACACTTAA
622 AAATATTAAAAC
1 AAATATTAAAAC
634 AAATATTAAAAC
1 AAATATTAAAAC
646 AA
1 AA
648 TAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:848 original size:12 final size:12
Alignment explanation
Indices: 833--922 Score: 82
Period size: 12 Copynumber: 7.8 Consensus size: 12
823 CCCAAACAAC
833 AAAAATAACAGT
1 AAAAATAACAGT
* *
845 AAAAACAACAAT
1 AAAAATAACAGT
857 AAAAATAAC---
1 AAAAATAACAGT
866 AAAAA-AACAGT
1 AAAAATAACAGT
** *
877 AAAAATAATTGG
1 AAAAATAACAGT
*
889 AAAAATAGA-AGC
1 AAAAATA-ACAGT
901 AAAAATAACAGT
1 AAAAATAACAGT
913 AAAAATAACA
1 AAAAATAACA
923 ACAAAAACAG
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
11 6 0.10
12 48 0.76
13 1 0.02
ACGTcount: A:0.70, C:0.09, G:0.08, T:0.13
Consensus pattern (12 bp):
AAAAATAACAGT
Found at i:849 original size:32 final size:32
Alignment explanation
Indices: 813--931 Score: 89
Period size: 32 Copynumber: 3.6 Consensus size: 32
803 AAAATGCATA
**
813 AAAAACAAC-ACCCAAACAACAAAAATAACAGT
1 AAAAACAACAACAAAAACAACAAAAA-AACAGT
* *
845 AAAAACAACAATAAAAATAACAAAAAAACAGT
1 AAAAACAACAACAAAAACAACAAAAAAACAGT
* * * *
877 AAAAATAATTGGAA-AAATAGAAGCAAAAATAACAGT
1 AAAAACAA---CAACAAAAACAA-CAAAAA-AACAGT
*
913 AAAAATAACAACAAAAACA
1 AAAAACAACAACAAAAACA
932 GTATGCTAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
32 22 0.32
33 14 0.20
34 11 0.16
35 8 0.12
36 14 0.20
ACGTcount: A:0.70, C:0.14, G:0.06, T:0.10
Consensus pattern (32 bp):
AAAAACAACAACAAAAACAACAAAAAAACAGT
Found at i:860 original size:24 final size:24
Alignment explanation
Indices: 827--929 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
817 ACAACACCCA
*
827 AACAACAAAAATAACAGTAAAAAC
1 AACAACAAAAATAACAGTAAAAAT
*
851 AACAATAAAAATAAC---AAAAA-
1 AACAACAAAAATAACAGTAAAAAT
** ** *
871 AACAGTAAAAATAATTGGAAAAAT
1 AACAACAAAAATAACAGTAAAAAT
*
895 AGA-AGCAAAAATAACAGTAAAAAT
1 A-ACAACAAAAATAACAGTAAAAAT
919 AACAACAAAAA
1 AACAACAAAAA
930 CAGTATGCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
20 13 0.20
21 5 0.08
23 6 0.09
24 40 0.62
25 1 0.02
ACGTcount: A:0.71, C:0.11, G:0.07, T:0.12
Consensus pattern (24 bp):
AACAACAAAAATAACAGTAAAAAT
Found at i:1381 original size:12 final size:12
Alignment explanation
Indices: 1364--1389 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1354 AAACACTTAA
1364 AAATATTAAAAC
1 AAATATTAAAAC
1376 AAATATTAAAAC
1 AAATATTAAAAC
1388 AA
1 AA
1390 TAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:1418 original size:20 final size:19
Alignment explanation
Indices: 1368--1419 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1358 ACTTAAAAAT
*
1368 ATTAAAACAAATATTAAAACA
1 ATTAAAA-AAAT-TGAAAACA
*
1389 A-TAAACAAATTGAAAACA
1 ATTAAAAAAATTGAAAACA
1407 CATTAAAAAAATT
1 -ATTAAAAAAATT
1420 TATACTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.27
19 5 0.19
20 13 0.50
21 1 0.04
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (19 bp):
ATTAAAAAAATTGAAAACA
Found at i:1575 original size:743 final size:693
Alignment explanation
Indices: 529--1966 Score: 1457
Period size: 743 Copynumber: 2.0 Consensus size: 693
519 GCCAAACACG
* *
529 AGTCCGGTGTGCCCCAACCCATATTATTATTTTTAGATTATTTTATTATATACAACAAATTTAAA
1 AGTCCGGTGTGACCCAACCCATATTATTATTTTTAGATTAATTTATTATATACAACAAATTTAAA
594 AAATATATAATATATCAAAAACACTTAAAAATATTAAAACAAATATTAAAACAATAAACAAATTG
66 AAATATATAATATATCAAAAACACTTAAAAATATTAAAACAAATATTAAAACAATAAACAAATTG
*
659 AAAATACATTAAAAAAATTATACTAAGATAGTTGCAACTAAAATAGCAACAGAATTAACAATAAA
131 AAAACACATTAAAAAAATTATACTAAGATAGTTGCAACTAAAATAGCAACAGAATTAACAATAAA
*
724 ACATAAGTTCTACAATATCCAAATAATAATAAAAACGATAGTGAAACAATATTAAAAACGGCAGC
196 ACATAAGTTCTACAATATCCAAATAATAATAAAAACGATAGTGAAACAACATTAAAAACGGCAGC
*
789 AAGAAAATATAAAAAAAATGCATAAAAAACAACACCCAAACAACAAAAATAACAGTAAAAACAAC
261 AAGAAAATATAAAAAAAATGCATAAAAAACAACACCCAAACAACAAAAATAACAGGAAAAACAAC
*
854 AATAAAAATAACAAAAAAACAGTAAAAATAATTGGAAAAATAGAAGCAAAAATAACAGTAAAAAT
326 AATAAAAATAACAAAAAAACAGTAAAAATAATTGGAAAAATAGAAGCAAAAACAACAGTAAAAAT
* * *
919 AACAACAAAAACAGTATGCTAACAACACTAAAACACTAGGAACAACAAAAAACAGCAAGATAATT
391 AACAACAAAAACAGTATACTAACAACACTAAAACACTAGGAACAAAAAAAAAAAGCAAGATAA-T
* *
984 TTTTTTCACAAATAATTAATTTATTCGAGCCAGGCTAGGCTCCAGCTGGAAAACTTTTACCCAAA
455 TTTTTTCAAAAATAATTAATTTATTCGAGCCAGGCTAGGCTCCAGCTGGAAAACCTTTACCCAAA
* * *
1049 GTCTAGCCCATTTAGAAAATGAGTTTCATTTTTTATCTAAACTCATTTTTTGGGCTTATATATA-
520 GTCTAACCCATTTAGAAAATGAGTTTCATTTTTTATCCAAACTCATTTTTTGGGCTTATACATAT
*
1113 TTTTTTTCAAATCTTCCTATTTTTCGAACAGTCCAATTCAGGTCTAGAATAAAATAAGGAGAAAG
585 TTTTTTTCAAATCTTCCTATTTTTCGAACAGTCCAACTCAGGTCTAGAATAAAATAAGGAGAAAG
*
1178 ATT-AAAAAAATTAAAAAATA-TATAAAAAAAATCTCACGTGAA
650 ATTAAAAAAAATTAAAAAAAAGTATAAAAAAAATCTCACGTGAA
**************************************** **** * **
1220 ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCCGGTGTGACCC
1 A-----------GTCCGGTGTGACCCAACCCATATTATTATTTTTAGATTAATTTATTAT-ATAC
* * **** * * * *
1285 AACCCATATTATTATTTTTAGATTAATTTATTCTATACAACAAATTTAAAAAAATATATAATATA
54 AA--CAAATT-TAAAAAATATA-TAATATA-TC-A-A-AA-ACACTT--AAAAATAT-TAA-A-A
* * * *
1350 TCAAAAACACTTAAAA-ATATTAAAACAAATATTAAAACAATAAACAAATTGAAAACACATTAAA
105 -C--AAATA-TTAAAACA-A-T-AAACAAAT-TGAAAAC-----AC--ATT-AAAA-AAATTATA
** * * * *
1414 AAAATTTATACTAAG-ATAGTTGCAACTAAAATAGCAACAGAATTAACAATAAAACATAAGTTCT
153 CTAA--GATAGT-TGCA-A----C-T--AAAATAGCAACAGAATTAACAATAAAACATAAGTTCT
* *
1478 ACAATATTCAAATAATAATAAAAACGATAGTGAAACAACATTAAAAACGGTAGCAAGAAAATAT-
207 ACAATATCCAAATAATAATAAAAACGATAGTGAAACAACATTAAAAACGGCAGCAAGAAAATATA
* * *
1542 AAAAAAATGCATAAAAAAACAACATCCAAACAACAAAAATAATAGGAAAAACAACAATATAAATA
272 AAAAAAATGCAT-AAAAAACAACACCCAAACAACAAAAATAACAGGAAAAACAACAATAAAAATA
*
1607 ACAAAAAAACATTAAAAATAATTGGAAAAATAGAAGCAAAAACAACAGTAAAAATAACAACAAAA
336 ACAAAAAAACAGTAAAAATAATTGGAAAAATAGAAGCAAAAACAACAGTAAAAATAACAACAAAA
*
1672 ACAGTATACTAACAACACTAAAACACTAGGAACAAAAAAAAAAAGCAAGATAATTTTTTTGAAAA
401 ACAGTATACTAACAACACTAAAACACTAGGAACAAAAAAAAAAAGCAAGATAATTTTTTTCAAAA
* * *
1737 ATAATTAATTTATTCGAGCTAGGCTAGGCTCGAGCTGGAAAACCTTTACCCAAGGTCTAACCCAT
466 ATAATTAATTTATTCGAGCCAGGCTAGGCTCCAGCTGGAAAACCTTTACCCAAAGTCTAACCCAT
1802 TTAGAAAATGAGTTTCATTTTTTATCCAAACTCATTTTTTGGGCTTATACATATTTTTTTTCAAA
531 TTAGAAAATGAGTTTCATTTTTTATCCAAACTCATTTTTTGGGCTTATACATATTTTTTTTCAAA
* * * *
1867 TCTTTCTATTTTTCGGATAGTCCAGCTCAGGTCTAGAATAAAATAAGGAGAAAGATTAAAAAAAA
596 TCTTCCTATTTTTCGAACAGTCCAACTCAGGTCTAGAATAAAATAAGGAGAAAGATTAAAAAAAA
1932 TTAAAAAAAAGTATAAAAAAAATCTCACGTGAA
661 TTAAAAAAAAGTATAAAAAAAATCTCACGTGAA
1965 AG
1 AG
1967 AGAAAGGAAA
Statistics
Matches: 593, Mismatches: 96, Indels: 73
0.78 0.13 0.10
Matches are distributed among these distances:
691 1 0.00
702 3 0.01
703 4 0.01
705 5 0.01
706 5 0.01
707 6 0.01
708 2 0.00
709 1 0.00
710 1 0.00
711 2 0.00
712 4 0.01
714 8 0.01
715 3 0.01
716 1 0.00
717 1 0.00
718 1 0.00
720 5 0.01
721 7 0.01
722 1 0.00
723 8 0.01
724 5 0.01
729 2 0.00
731 3 0.01
732 4 0.01
733 8 0.01
735 5 0.01
736 2 0.00
740 1 0.00
742 133 0.22
743 322 0.54
744 16 0.03
745 23 0.04
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.25
Consensus pattern (693 bp):
AGTCCGGTGTGACCCAACCCATATTATTATTTTTAGATTAATTTATTATATACAACAAATTTAAA
AAATATATAATATATCAAAAACACTTAAAAATATTAAAACAAATATTAAAACAATAAACAAATTG
AAAACACATTAAAAAAATTATACTAAGATAGTTGCAACTAAAATAGCAACAGAATTAACAATAAA
ACATAAGTTCTACAATATCCAAATAATAATAAAAACGATAGTGAAACAACATTAAAAACGGCAGC
AAGAAAATATAAAAAAAATGCATAAAAAACAACACCCAAACAACAAAAATAACAGGAAAAACAAC
AATAAAAATAACAAAAAAACAGTAAAAATAATTGGAAAAATAGAAGCAAAAACAACAGTAAAAAT
AACAACAAAAACAGTATACTAACAACACTAAAACACTAGGAACAAAAAAAAAAAGCAAGATAATT
TTTTTCAAAAATAATTAATTTATTCGAGCCAGGCTAGGCTCCAGCTGGAAAACCTTTACCCAAAG
TCTAACCCATTTAGAAAATGAGTTTCATTTTTTATCCAAACTCATTTTTTGGGCTTATACATATT
TTTTTTCAAATCTTCCTATTTTTCGAACAGTCCAACTCAGGTCTAGAATAAAATAAGGAGAAAGA
TTAAAAAAAATTAAAAAAAAGTATAAAAAAAATCTCACGTGAA
Found at i:1612 original size:20 final size:20
Alignment explanation
Indices: 1588--1627 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1578 AAATAATAGG
*
1588 AAAAACAACAATATAAATAAC
1 AAAAA-AACAATAAAAATAAC
*
1609 AAAAAAACATTAAAAATAA
1 AAAAAAACAATAAAAATAA
1628 TTGGAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAAAACAATAAAAATAAC
Found at i:1948 original size:12 final size:10
Alignment explanation
Indices: 1921--1954 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
1911 AAGGAGAAAG
1921 ATTAAAAAAA
1 ATTAAAAAAA
1931 ATTAAAAAAA
1 ATTAAAAAAA
1941 AGTATAAAAAAA
1 A-T-TAAAAAAA
1953 AT
1 AT
1955 CTCACGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.50
11 2 0.09
12 9 0.41
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
ATTAAAAAAA
Done.