Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003035.1 Kokia drynarioides strain JFW-HI SEQ_115557, 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: 28050
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:572 original size:30 final size:29
Alignment explanation
Indices: 502--879 Score: 342
Period size: 29 Copynumber: 12.9 Consensus size: 29
492 CCCTGAAGGT
*
502 CCCT-AAACTGTCC-AAAATTCTATTTTTA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTA
** * *
530 CCAC-CGAACTTCCCAAAATCCCATTTTTGA
1 CC-CTAAAACTTCCAAAAATTCCATTTTT-A
560 CCCTAAAACTTCCAAAAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
* * *
589 CTCTCAAACTTCCAAAAATCCCATTTTTTA
1 CCCTAAAACTTCCAAAAATTCCA-TTTTTA
* *
619 CCCCAAAACTTCCAAAAATTTCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
** *
648 CCCTTGAACTT-CAAAAATCCCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTT-A
*
677 CCCTAAAACTTCAAAAAATTCCA-TTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
705 CACCT-AAAC-TCCTAAAAA-TCTCATTTTTGA
1 C-CCTAAAACTTCC-AAAAATTC-CATTTTT-A
* *
735 CCCCAAAACTTCCAAAAATTCCACTTTTGA
1 CCCTAAAACTTCCAAAAATTCCA-TTTTTA
*
765 CCCTAAAACTTACAAAAATTCCA-TTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
* *
793 CCCCCAAAACTTCCAAAAATTTCATTTTTA
1 -CCCTAAAACTTCCAAAAATTCCATTTTTA
*** * *
823 CCCCCGAACATCCAAAAATTCCATTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
** *
852 CCCTAAATTTTCCCAAAATTACCATTTT
1 CCCTAAAACTTCCAAAAATT-CCATTTT
880 GCCCCCAAGT
Statistics
Matches: 285, Mismatches: 45, Indels: 38
0.77 0.12 0.10
Matches are distributed among these distances:
27 4 0.01
28 36 0.13
29 133 0.47
30 103 0.36
31 9 0.03
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTA
Found at i:604 original size:58 final size:59
Alignment explanation
Indices: 502--879 Score: 387
Period size: 58 Copynumber: 6.5 Consensus size: 59
492 CCCTGAAGGT
* * * *
502 CCCT-AAACTGTCC-AAAATTCTATTTTTACCAC-CGAACTTCCCAAAATCCCATTTTTGA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTACC-CTCAAACTTCCAAAAATCCCATTTTTAA
* *
560 CCCTAAAACTTCCAAAAATTCCATTTTTACTCTCAAACTTCCAAAAATCCCATTTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAA
* * **
619 CCCCAAAACTTCCAAAAATTTCATTTTTACCCTTGAACTT-CAAAAATCCCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAA
* * *
677 CCCTAAAACTTCAAAAAATTCCA-TTTTACACCT-AAAC-TCCTAAAAATCTCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTAC-CCTCAAACTTCC-AAAAATCCCATTTTTAA
* * * * * *
735 CCCCAAAACTTCCAAAAATTCCACTTTTGACCCTAAAACTTACAAAAATTCCA-TTTTAC
1 CCCTAAAACTTCCAAAAATTCCA-TTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAA
* * * * * *
794 CCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGAACATCCAAAAATTCCA-TTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAA
** *
852 CCCTAAATTTTCCCAAAATTACCATTTT
1 CCCTAAAACTTCCAAAAATT-CCATTTT
880 GCCCCCAAGT
Statistics
Matches: 271, Mismatches: 38, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
56 1 0.00
57 10 0.04
58 128 0.47
59 113 0.42
60 17 0.06
61 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAA
Found at i:908 original size:88 final size:85
Alignment explanation
Indices: 502--887 Score: 339
Period size: 88 Copynumber: 4.4 Consensus size: 85
492 CCCTGAAGGT
* * * * * *
502 CCCT-AAACTGTCC-AAAATTCTATTTTTACCACCGAACTTCCCAAAATCCCATTTTTGACCCTA
1 CCCTAAAACT-TCCAAAAATTCCA-TTTTACCCCCAAAC-TCCAAAAATCTCATTTTT-ACCCCA
* *
565 AAACTTCCAAAAATTCCA-TTTTTA
62 GAAC-TCCAAAAATTCCACTTTTAA
* * * * * **
589 CTCTCAAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTTCATTTTTACCCTTG
1 CCCTAAAACTTCCAAAAATTCCA--TTTTACCCCCAAAC-TCCAAAAATCTCATTTTTACCCCAG
* * *
654 AACTTCAAAAATCCCATTTTTAA
63 AACTCCAAAAATTCCACTTTTAA
* * * *
677 CCCTAAAACTTCAAAAAATTCCATTTTACACCTAAACTCCTAAAAATCTCATTTTTGACCCCAAA
1 CCCTAAAACTTCCAAAAATTCCATTTTACCCCCAAACTCC-AAAAATCTCATTTTT-ACCCCAGA
*
742 ACTTCCAAAAATTCCACTTTTGA
64 AC-TCCAAAAATTCCACTTTTAA
* * *
765 CCCTAAAACTTACAAAAATTCCATTTTACCCCCAAAACTTCCAAAAATTTCATTTTTACCCCCGA
1 CCCTAAAACTTCCAAAAATTCCATTTTACCCCC-AAAC-TCCAAAAATCTCATTTTTACCCCAGA
830 ACATCCAAAAATTCCA-TTTTAA
64 AC-TCCAAAAATTCCACTTTTAA
** * *
852 CCCTAAATTTTCCCAAAATTACCATTTTGCCCCCAA
1 CCCTAAAACTTCCAAAAATT-CCATTTTACCCCCAA
888 GTATCCGAAA
Statistics
Matches: 247, Mismatches: 42, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
85 3 0.01
86 26 0.11
87 47 0.19
88 122 0.49
89 46 0.19
90 3 0.01
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (85 bp):
CCCTAAAACTTCCAAAAATTCCATTTTACCCCCAAACTCCAAAAATCTCATTTTTACCCCAGAAC
TCCAAAAATTCCACTTTTAA
Found at i:4027 original size:16 final size:15
Alignment explanation
Indices: 3989--4018 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3979 TTTGAGTATT
3989 TATATTTTAATTTTA
1 TATATTTTAATTTTA
4004 TATAATTTTAATTTT
1 TAT-ATTTTAATTTT
4019 TTCATATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 3 0.21
16 11 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTTAATTTTA
Found at i:4980 original size:30 final size:31
Alignment explanation
Indices: 4945--5011 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4935 AAAATTAATA
* *
4945 ATTTAATTAATAAATTATTC-GAAAATTTTC
1 ATTTAACTAATAAATTATTCAAAAAATTTTC
*
4975 ATTTAAACTAGTAAATTATTCAAAAAATTTTC
1 ATTT-AACTAATAAATTATTCAAAAAATTTTC
5007 -TTTAA
1 ATTTAA
5012 ATTATTGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 6 0.19
31 17 0.53
32 9 0.28
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTTAACTAATAAATTATTCAAAAAATTTTC
Found at i:5898 original size:18 final size:18
Alignment explanation
Indices: 5875--5917 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5865 ATTCAATGTG
5875 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
5893 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
5911 TAATTAA
1 TAATTAA
5918 AACCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:6141 original size:3 final size:3
Alignment explanation
Indices: 6133--6158 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6123 CCTTATTAGA
6133 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6159 CAACAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17118 original size:23 final size:22
Alignment explanation
Indices: 17088--17134 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
17078 TATTTTGCCC
17088 TCAGTTAAATTTTACTATATTTT
1 TCAGTTAAATTTTACTAT-TTTT
*
17111 TCAGTTAAATTTTATTATTTTT
1 TCAGTTAAATTTTACTATTTTT
17133 TC
1 TC
17135 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (22 bp):
TCAGTTAAATTTTACTATTTTT
Found at i:18933 original size:28 final size:26
Alignment explanation
Indices: 18897--18952 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
18887 TCTATAATAG
18897 AAAGAAAATTTAAGTATTAAAATGAGAA
1 AAAGAAAA--TAAGTATTAAAATGAGAA
* *
18925 AAAGAAAATAGGTATTAAAGTGAGAA
1 AAAGAAAATAAGTATTAAAATGAGAA
18951 AA
1 AA
18953 TAAAGAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 18 0.69
28 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (26 bp):
AAAGAAAATAAGTATTAAAATGAGAA
Found at i:24840 original size:19 final size:18
Alignment explanation
Indices: 24816--24862 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
24806 ATTATGATAA
24816 ATTTAAATTTATATAGTAT
1 ATTTAAATTTATATA-TAT
24835 ATTTAAA-TTAT-TATAT
1 ATTTAAATTTATATATAT
24851 -TTTAAATTTATA
1 ATTTAAATTTATA
24863 ATAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.23
16 7 0.27
17 2 0.08
18 4 0.15
19 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTTAAATTTATATATAT
Found at i:26835 original size:17 final size:17
Alignment explanation
Indices: 26813--26851 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
26803 AAAAAATTCG
26813 ATTAAAAATTT-AATAA
1 ATTAAAAATTTAAATAA
*
26829 TATTAAATATTTAAATAA
1 -ATTAAAAATTTAAATAA
26847 ATTAA
1 ATTAA
26852 TAACATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAAAATTTAAATAA
Found at i:27476 original size:20 final size:21
Alignment explanation
Indices: 27451--27490 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
27441 ATCTCTTTGT
27451 ATCCAAAAG-AAAAATGTTTA
1 ATCCAAAAGTAAAAATGTTTA
*
27471 ATCCAAAAGTAAAACTGTTT
1 ATCCAAAAGTAAAAATGTTT
27491 GAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (21 bp):
ATCCAAAAGTAAAAATGTTTA
Done.