Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010107.1 Kokia drynarioides strain JFW-HI SEQ_124893, 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: 42400
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 301 characters in sequence are not A, C, G, or T
Found at i:585 original size:29 final size:30
Alignment explanation
Indices: 527--996 Score: 438
Period size: 30 Copynumber: 15.8 Consensus size: 30
517 CAAGATGTCC
*
527 CGAAACTTTCAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
*
557 CGAAACTTCCAAAAATTCCA-TTTTAACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
*
586 CGAAACTTCCAAAAATTTCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
*
616 C-AAACTTTCAAAAATTCCATTTTTGACC-
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* *
644 CTGAAACTTCCAAAAAAAT-AATTTTT-ACCCT
1 C-GAAACTTCC-AAAAATTCCATTTTTGA-CCT
675 CG-AACTTCCAAAAATTCCATTTTTGACC-
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* *
703 CTGAAACTTCCAAAAATTACATTTTT-ACCCC
1 C-GAAACTTCCAAAAATTCCATTTTTGA-CCT
* **
734 CG-AACTTCAAAAAAATTCCATTTTTTTCCT
1 CGAAACTTC-CAAAAATTCCATTTTTGACCT
*
764 CGAAACTTCCAAAAAATTCCATTTTTGACCC
1 CGAAACTTCC-AAAAATTCCATTTTTGACCT
* *
795 CTAAACTTTCAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
**
825 TAAAACTTCCAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* *
855 CGAAACTTTC-AAAATTACCATTTTT--CCC
1 CGAAACTTCCAAAAATT-CCATTTTTGACCT
* * * * *
883 CCAGA-TGTCCAAAAATTCTATTTTCGACCA
1 CGAAACT-TCCAAAAATTCCATTTTTGACCT
913 CGAAAC-TCCAAAAATTCCATTTTT-ACTCT
1 CGAAACTTCCAAAAATTCCATTTTTGAC-CT
* *
942 CG-AA-TGTCTAAAAATTCCATCTTTTAACCT
1 CGAAACT-TCCAAAAATTCCAT-TTTTGACCT
*
972 CG-AACTTCCCCAAAATTACCATTTT
1 CGAAACTT-CCAAAAATT-CCATTTT
997 GCCCCCGGGT
Statistics
Matches: 365, Mismatches: 43, Indels: 63
0.77 0.09 0.13
Matches are distributed among these distances:
27 1 0.00
28 25 0.07
29 119 0.33
30 164 0.45
31 52 0.14
32 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (30 bp):
CGAAACTTCCAAAAATTCCATTTTTGACCT
Found at i:650 original size:59 final size:61
Alignment explanation
Indices: 528--936 Score: 417
Period size: 59 Copynumber: 6.9 Consensus size: 61
518 AAGATGTCCC
* * *
528 GAAACTTTCAAAAATTCCATTTTTGA-CCTCGAAACTTCCAAAAATTCCA-TTTT-AACCT
1 GAAACTTCCAAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATTCCATTTTTGACCCT
*
586 CGAAACTTCCAAAAATTTCATTTTT-ACCCTC-AAACTTTCAAAAATTCCATTTTTGACCCT
1 -GAAACTTCCAAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATTCCATTTTTGACCCT
* * *
646 GAAACTTCCAAAAAAAT-AATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCT
1 GAAACTTCC-AAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATTCCATTTTTGACCCT
* * **
705 GAAACTTCCAAAAATTACATTTTT-ACCCCCG-AAC-TTCAAAAAAATTCCATTTTT-TTCCT
1 GAAACTTCCAAAAATTCCATTTTTGACCCTCGAAACTTTC--AAAAATTCCATTTTTGACCCT
* *
764 CGAAACTTCCAAAAAATTCCATTTTTGACCC-CTAAACTTTCAAAAATTCCATTTTTGACCTT
1 -GAAACTTCC-AAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATTCCATTTTTGACCCT
* *
826 AAAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTTTC-AAAATTACCATTTTT--CCCC
1 GAAACTTCCAAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATT-CCATTTTTGACCCT
* * * * * *
884 CAGA-TGTCCAAAAATTCTATTTTCGA-CCACGAAAC-TCCAAAAATTCCATTTTT
1 GAAACT-TCCAAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATTCCATTTTT
937 ACTCTCGAAT
Statistics
Matches: 304, Mismatches: 28, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
57 11 0.04
58 62 0.20
59 113 0.37
60 68 0.22
61 38 0.12
62 9 0.03
63 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (61 bp):
GAAACTTCCAAAAATTCCATTTTTGACCCTCGAAACTTTCAAAAATTCCATTTTTGACCCT
Found at i:2724 original size:24 final size:22
Alignment explanation
Indices: 2689--2732 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
2679 ATTTTTTTTT
2689 TTAAAAATATTTCAAT-TTTTAA
1 TTAAAAATATTT-AATATTTTAA
2711 TTAAAAATCAATTTAATATTTT
1 TTAAAAAT--ATTTAATATTTT
2733 CTACAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAAATATTTAATATTTTAA
Found at i:6246 original size:18 final size:20
Alignment explanation
Indices: 6203--6248 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
6193 ATTATTAAAT
6203 TATTTTATTATTTAATATTA
1 TATTTTATTATTTAATATTA
6223 TAATTTTA-T-TTTAATCA-TA
1 T-ATTTTATTATTTAAT-ATTA
6242 TATTTTA
1 TATTTTA
6249 ACAATAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 3 0.12
21 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTATTATTTAATATTA
Found at i:7324 original size:26 final size:27
Alignment explanation
Indices: 7280--7331 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
7270 AATTCAATAA
* *
7280 ATTATTAAATTTTTTAATTAAATATTC
1 ATTATTAAATTTATGAATTAAATATTC
*
7307 ATTA-TAAATTTATGAATTAATTATT
1 ATTATTAAATTTATGAATTAAATATT
7332 TGAATTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTATTAAATTTATGAATTAAATATTC
Found at i:8407 original size:14 final size:14
Alignment explanation
Indices: 8390--8419 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8380 ATATTCAAAC
8390 AATAATAACATAAT
1 AATAATAACATAAT
*
8404 AATAATAATATAAT
1 AATAATAACATAAT
8418 AA
1 AA
8420 CAAAATGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAACATAAT
Found at i:25492 original size:17 final size:16
Alignment explanation
Indices: 25470--25508 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
25460 AAATAAAAAT
25470 ATTTTTATATTTTTTAA
1 ATTTTTA-ATTTTTTAA
*
25487 ATTTTTAATTTTTTTA
1 ATTTTTAATTTTTTAA
25503 ATTTTT
1 ATTTTT
25509 GAATGATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTAATTTTTTAA
Found at i:25780 original size:18 final size:19
Alignment explanation
Indices: 25745--25782 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
25735 TTGTATGTCT
25745 TAAAAATACATAATATATA
1 TAAAAATACATAATATATA
*
25764 TAAAAATAATATAATATAT
1 TAAAAAT-ACATAATATAT
25783 TACAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAAAATACATAATATATA
Found at i:29318 original size:27 final size:27
Alignment explanation
Indices: 29273--29326 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
29263 CATTTAAGCC
29273 CTTCTTCTTTTTTTTTTTTTTCTTGCA
1 CTTCTTCTTTTTTTTTTTTTTCTTGCA
29300 NCTTCTT-TTTTTTTTTTTTTTCTTGCA
1 -CTTCTTCTTTTTTTTTTTTTTCTTGCA
29327 GTCAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (27 bp):
CTTCTTCTTTTTTTTTTTTTTCTTGCA
Found at i:29719 original size:38 final size:37
Alignment explanation
Indices: 29677--29765 Score: 85
Period size: 38 Copynumber: 2.4 Consensus size: 37
29667 AAAAATTATT
29677 AAATTTTAATAAAAT-AAATAAAAATAAAATTTATAAAA
1 AAATTTTAATAAAATAAAATAAAAA-AAAA-TTATAAAA
** ***
29715 AAATTAGAAATAAAATAAAATCGTAAAAAATTATAAAA
1 AAATT-TTAATAAAATAAAATAAAAAAAAATTATAAAA
29753 AAA-TTT-ATAAAAT
1 AAATTTTAATAAAAT
29766 TCTATAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
35 7 0.17
37 1 0.02
38 16 0.38
39 12 0.29
40 6 0.14
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (37 bp):
AAATTTTAATAAAATAAAATAAAAAAAAATTATAAAA
Found at i:29725 original size:24 final size:25
Alignment explanation
Indices: 29676--29730 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
29666 TAAAAATTAT
*
29676 TAAATTTTAATAAAATAAATAAAAA
1 TAAAATTTAATAAAATAAATAAAAA
*
29701 TAAAATTT-ATAAAA-AAATTAGAAA
1 TAAAATTTAATAAAATAAA-TAAAAA
29725 TAAAAT
1 TAAAAT
29731 AAAATCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 17 0.63
25 7 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TAAAATTTAATAAAATAAATAAAAA
Found at i:29732 original size:44 final size:45
Alignment explanation
Indices: 29640--29735 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 45
29630 AAAAAATTAT
* * **
29640 AATAAAA-AAAAAACAAATAAAAGTTATAAAAATTATTAAATTTT
1 AATAAAATAAAAAACAAATAAAAGTTATAAAAATAATTAAAATAA
* *
29684 AATAAAATAAATAA-AAATAAAATTTATAAAAA-AATTAGAAATAA
1 AATAAAATAAAAAACAAATAAAAGTTATAAAAATAATTA-AAATAA
29728 AATAAAAT
1 AATAAAAT
29736 CGTAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
43 4 0.09
44 35 0.80
45 5 0.11
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (45 bp):
AATAAAATAAAAAACAAATAAAAGTTATAAAAATAATTAAAATAA
Found at i:29760 original size:12 final size:11
Alignment explanation
Indices: 29739--29795 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
29729 ATAAAATCGT
29739 AAAAAATTATA
1 AAAAAATTATA
29750 AAAAAATT-T-
1 AAAAAATTATA
* *
29759 ATAAAATTCTA
1 AAAAAATTATA
* *
29770 TAAAAATCATA
1 AAAAAATTATA
29781 AAAGAAATTATA
1 AAA-AAATTATA
29793 AAA
1 AAA
29796 TGCATCAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 7 0.19
10 2 0.06
11 17 0.47
12 10 0.28
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:29998 original size:18 final size:19
Alignment explanation
Indices: 29965--30022 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
29955 TTAATACTAT
*
29965 AATTTTAATCATTTTTTATG
1 AATTTT-ATAATTTTTTATG
* *
29985 AATTTTATATTTTTTTA-C
1 AATTTTATAATTTTTTATG
*
30003 ATTTTTATAATTTTTTATG
1 AATTTTATAATTTTTTATG
30022 A
1 A
30023 CTTTATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
AATTTTATAATTTTTTATG
Found at i:30027 original size:18 final size:18
Alignment explanation
Indices: 29975--30030 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
29965 AATTTTAATC
29975 ATTTTTTATGAATTTTATA
1 ATTTTTTATG-ATTTTATA
* *
29994 TTTTTTTA-CATTTTTATA
1 ATTTTTTATGA-TTTTATA
*
30012 ATTTTTTATGACTTTATA
1 ATTTTTTATGATTTTATA
30030 A
1 A
30031 AATTTATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.03
18 21 0.70
19 8 0.27
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
ATTTTTTATGATTTTATA
Found at i:30045 original size:38 final size:37
Alignment explanation
Indices: 30003--30086 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 37
29993 ATTTTTTTAC
* *
30003 ATTTTTATAATTTTTTATGACTTTATA-AAA-TTTATATT
1 ATTTTTAT-ATATTTAATG-CTTTATATAAATTTTAT-TT
*
30041 ATTTTCTATATATTTAATGCTTTTTATAAATTTTATTT
1 ATTTT-TATATATTTAATGCTTTATATAAATTTTATTT
30079 ATTTTTAT
1 ATTTTTAT
30087 TTTTTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
37 9 0.22
38 23 0.57
39 8 0.20
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (37 bp):
ATTTTTATATATTTAATGCTTTATATAAATTTTATTT
Found at i:30083 original size:19 final size:18
Alignment explanation
Indices: 30003--30086 Score: 55
Period size: 19 Copynumber: 4.4 Consensus size: 18
29993 ATTTTTTTAC
30003 ATTTTTAT-AATTT-TTT
1 ATTTTTATAAATTTATTT
*
30019 ATGACTTTATAAAATTTATATT
1 AT--TTTTAT-AAATTTAT-TT
* * *
30041 ATTTTCTATATATTTAATG
1 ATTTT-TATAAATTTATTT
*
30060 CTTTTTATAAATTTTATTT
1 ATTTTTATAAA-TTTATTT
30079 ATTTTTAT
1 ATTTTTAT
30087 TTTTTATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.04
18 10 0.20
19 17 0.34
20 13 0.26
21 4 0.08
22 4 0.08
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTATAAATTTATTT
Done.