Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011234.1 Kokia drynarioides strain JFW-HI SEQ_126212, 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: 76185
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 68 characters in sequence are not A, C, G, or T
Found at i:1261 original size:71 final size:71
Alignment explanation
Indices: 1145--1276 Score: 212
Period size: 71 Copynumber: 1.9 Consensus size: 71
1135 TTTGAATATG
* *
1145 GGGTCATGGTCATAGTTGATCGTCGCTTGTTGGATTCCTTCTCCTTAAAGAAGATTCAAATTCTG
1 GGGTCATGGTCATAGTTAATCGTCGCTTCTTGGATTCCTTCTCCTTAAAGAAGATTCAAATTCTG
1210 ATTATT
66 ATTATT
* *
1216 GGGTCATGGTCAT-GATTAATCGTCGCTTCTTGGATTCTTTCTCCTTAAAGAGGATTCAAAT
1 GGGTCATGGTCATAG-TTAATCGTCGCTTCTTGGATTCCTTCTCCTTAAAGAAGATTCAAAT
1277 GTTGATAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
70 1 0.02
71 55 0.98
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (71 bp):
GGGTCATGGTCATAGTTAATCGTCGCTTCTTGGATTCCTTCTCCTTAAAGAAGATTCAAATTCTG
ATTATT
Found at i:5592 original size:18 final size:18
Alignment explanation
Indices: 5569--5607 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5559 TGATGTTGGA
5569 TTTC-TTTCCTTTTTGTTT
1 TTTCTTTTCCTTTTT-TTT
*
5587 TTTCTTTTTCTTTTTTTT
1 TTTCTTTTCCTTTTTTTT
5605 TTT
1 TTT
5608 TTGTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (18 bp):
TTTCTTTTCCTTTTTTTT
Found at i:12114 original size:21 final size:21
Alignment explanation
Indices: 12090--12132 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12080 GAGTCGATGG
*
12090 GTGA-TATGAAGTCAGCTCTCT
1 GTGATTATGAAG-CAGCACTCT
*
12111 GTGATTGTGAAGCAGCACTCT
1 GTGATTATGAAGCAGCACTCT
12132 G
1 G
12133 CTTGGAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGATTATGAAGCAGCACTCT
Found at i:19681 original size:30 final size:31
Alignment explanation
Indices: 19640--19706 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
19630 GTTTACATTT
*
19640 CAGTCCCTCAAC-TTTGAAAATGTGACAAAA
1 CAGTCCCTCAACTTTTGAAAATATGACAAAA
*
19670 CAGTTCCTCAACTTTTGAAAATATGACAAAA
1 CAGTCCCTCAACTTTTGAAAATATGACAAAA
19701 CAGTCC
1 CAGTCC
19707 TTTAACATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (31 bp):
CAGTCCCTCAACTTTTGAAAATATGACAAAA
Found at i:19832 original size:30 final size:31
Alignment explanation
Indices: 19796--19867 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
19786 ATTACGTTTA
* * * *
19796 ACAAAACAGTCACTCAACTT-TGGAAATGTG
1 ACAAAACAGTCACTAAAATTATCGAAAAGTG
19826 ACAAAACAGTCACTAAAATTATCGAAAAGTG
1 ACAAAACAGTCACTAAAATTATCGAAAAGTG
*
19857 ACAAAATAGTC
1 ACAAAACAGTC
19868 TTTTTGTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATCGAAAAGTG
Found at i:26981 original size:17 final size:17
Alignment explanation
Indices: 26959--27045 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
26949 TAAACTCCCT
26959 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
26976 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
*
26993 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* *
27011 TTAAATTTAATTT-AAG
1 TTAAATTTATTTTAAAA
* *
27027 TTAAAATTATTTTCAAA
1 TTAAATTTATTTTAAAA
27044 TT
1 TT
27046 TAAAATTATC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
16 13 0.22
17 31 0.53
18 14 0.24
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:27009 original size:11 final size:11
Alignment explanation
Indices: 26991--27048 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
26981 TTTGTTTAAA
26991 AATTTAAATTT
1 AATTTAAATTT
*
27002 ATTTTAAATTT
1 AATTTAAATTT
27013 AAATTT-AATTT
1 -AATTTAAATTT
* *
27024 AAGTTAAAATT
1 AATTTAAATTT
*
27035 ATTTTCAAATTT
1 AATTT-AAATTT
27047 AA
1 AA
27049 AATTATCATA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
10 4 0.11
11 22 0.61
12 10 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:27063 original size:17 final size:18
Alignment explanation
Indices: 27027--27068 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
27017 TTAATTTAAG
**
27027 TTAAAATTATTTTCAAAT
1 TTAAAATTATCATCAAAT
27045 TTAAAATTATCAT-AAAT
1 TTAAAATTATCATCAAAT
27062 TTAAAAT
1 TTAAAAT
27069 AAATAAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAAATTATCATCAAAT
Found at i:28933 original size:29 final size:29
Alignment explanation
Indices: 28890--29242 Score: 349
Period size: 29 Copynumber: 12.0 Consensus size: 29
28880 CCCCAGAGGT
28890 CCCT-AAACTGTCCAAAAATTCCATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
* *
28919 CCCTCGAACTTCCAAAAATCCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* **
28948 ACCTCGAAACTTCCAAAAATTTTATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
*
28978 CCCTCAAACTTTCAAAAA-TCTCATTTTTGA
1 CCCTCAAACTTCCAAAAATTC-CATTTTT-A
29008 -CCTCAAAACTTCCAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* * * *
29037 CCCTCGAACTTTCGAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
*** *
29067 CCAAAAAACTTCCAAAAATTCTATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* * ** *
29096 CCCTTAAATTTTTAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
29126 CCC-CAAAACTTCCAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
29155 -CCTCCAAACTTTCAAAAATCCCATTTTTGA
1 CCCT-CAAACTTCCAAAAATTCCATTTTT-A
*
29185 -CCTCGAAACTTCCAAAAATTACATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
29214 CCCCCAAACTTCCAAAAATCCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
29243 ACCCCGAATT
Statistics
Matches: 264, Mismatches: 45, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.01
29 135 0.51
30 124 0.47
31 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:29272 original size:30 final size:29
Alignment explanation
Indices: 29120--29276 Score: 97
Period size: 29 Copynumber: 5.3 Consensus size: 29
29110 AAAATCCCAT
* *
29120 TTTTGACCCCAAAACTTCCAAAAATT-CCA
1 TTTT-ACCCCCAAACTTCCCAAAATTACCA
* * * *
29149 TTTTTACCTCCAAACTT-TCAAAAATCCCA
1 -TTTTACCCCCAAACTTCCCAAAATTACCA
* * *
29178 TTTTTGACCTCGAAACTTCCAAAAATTA-CA
1 -TTTT-ACCCCCAAACTTCCCAAAATTACCA
* *
29208 TTTTTACCCCCAAACTT-CCAAAAATCCCA
1 -TTTTACCCCCAAACTTCCCAAAATTACCA
* **
29237 TTTTTAACCCCGAATTTTCCCAAAATTACCA
1 -TTTT-ACCCCCAAACTTCCCAAAATTACCA
29268 TTTTACCCC
1 TTTTACCCC
29277 TTGGTATCCG
Statistics
Matches: 101, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
28 11 0.11
29 40 0.40
30 35 0.35
31 15 0.15
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
TTTTACCCCCAAACTTCCCAAAATTACCA
Found at i:29276 original size:59 final size:59
Alignment explanation
Indices: 28894--29241 Score: 491
Period size: 59 Copynumber: 5.9 Consensus size: 59
28884 AGAGGTCCCT
* * * *
28894 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCTCA
** *
28954 AAACTTCCAAAAATTTTATTTTTACCCTCAAACTTTCAAAAATCTCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCTCA
* * **
29013 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCGAAAATCCCATTTTTGACCAAA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCTCA
* * * * *
29072 AAACTTCCAAAAATTCTATTTTTACCCTTAAATTTTTAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCTCA
*
29131 AAACTTCCAAAAATTCCATTTTTA-CCTCCAAACTTTCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCT-CAAACTTTCAAAAATCCCATTTTTGACCTCA
* * *
29190 AAACTTCCAAAAATTACATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTT
29242 AACCCCGAAT
Statistics
Matches: 255, Mismatches: 31, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
58 3 0.01
59 245 0.96
60 7 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTGACCTCA
Found at i:52810 original size:17 final size:18
Alignment explanation
Indices: 52769--52802 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52759 TAAAAATTGT
52769 AATAATTATATATTTAAA
1 AATAATTATATATTTAAA
52787 AATAATTATA-ATTTAA
1 AATAATTATATATTTAA
52803 TATAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAATTATATATTTAAA
Found at i:52810 original size:44 final size:46
Alignment explanation
Indices: 52756--52849 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
52746 AAAAATTAGA
52756 TAATAAAAATTGTAAT-AAT-T-ATATATTTAAAAATAATTATAATT
1 TAATAAAAATTGTAATAAATATGATATATTTAAAAAT-ATTATAATT
* * * *
52800 TAATATAAATTGTGATAAATATGTTATATTTTAAAATATTATAATT
1 TAATAAAAATTGTAATAAATATGATATATTTAAAAATATTATAATT
52846 TAAT
1 TAAT
52850 TTATAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 14 0.33
45 3 0.07
46 14 0.33
47 12 0.28
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (46 bp):
TAATAAAAATTGTAATAAATATGATATATTTAAAAATATTATAATT
Found at i:53438 original size:16 final size:16
Alignment explanation
Indices: 53414--53448 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53404 TTTTTTTTAC
*
53414 TTATGGTTGAAATTAT
1 TTATAGTTGAAATTAT
53430 TTATAGTTGAAATTAT
1 TTATAGTTGAAATTAT
53446 TTA
1 TTA
53449 AAAATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (16 bp):
TTATAGTTGAAATTAT
Found at i:53669 original size:26 final size:27
Alignment explanation
Indices: 53622--53679 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
53612 AAACACAATT
*
53622 AAAA-ATAATAGAAAATACAAATTTTA
1 AAAATATAATAGAAAATACAAATTATA
* *
53648 AAAATATAATATATAATA-AAATTATA
1 AAAATATAATAGAAAATACAAATTATA
*
53674 TAAATA
1 AAAATA
53680 ATTTAATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATATAATAGAAAATACAAATTATA
Found at i:65360 original size:76 final size:76
Alignment explanation
Indices: 65267--65415 Score: 280
Period size: 76 Copynumber: 2.0 Consensus size: 76
65257 GCAAATTAAT
*
65267 AGCATAAATTCCTTCATTATATAGTGGTTAATGGATGTTCTATGGTTTGCTTTTGTGGCTCTATT
1 AGCATAAATCCCTTCATTATATAGTGGTTAATGGATGTTCTATGGTTTGCTTTTGTGGCTCTATT
65332 GGAATCATGAA
66 GGAATCATGAA
*
65343 AGCATAAATCCCTTCATTATATAGTGGTTAATGGATGTTTTATGGTTTGCTTTTGTGGCTCTATT
1 AGCATAAATCCCTTCATTATATAGTGGTTAATGGATGTTCTATGGTTTGCTTTTGTGGCTCTATT
65408 GGAATCAT
66 GGAATCAT
65416 TAATTTTATT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (76 bp):
AGCATAAATCCCTTCATTATATAGTGGTTAATGGATGTTCTATGGTTTGCTTTTGTGGCTCTATT
GGAATCATGAA
Found at i:71698 original size:14 final size:14
Alignment explanation
Indices: 71679--71705 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
71669 GAAATTCAAA
71679 TAAAAAATTATATT
1 TAAAAAATTATATT
71693 TAAAAAATTATAT
1 TAAAAAATTATAT
71706 ACAAAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAAAATTATATT
Found at i:73001 original size:6 final size:6
Alignment explanation
Indices: 72982--73060 Score: 63
Period size: 6 Copynumber: 13.2 Consensus size: 6
72972 AATCAAATCC
* * * *
72982 AATCAA AATCGAA AATGAA AATCAA AATCAA AATC-G AAT-AA ACTCTA
1 AATCAA AATC-AA AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA
* * *
73029 AATCAAA AATCAC AATCAA TATCAA CATCAA A
1 AATC-AA AATCAA AATCAA AATCAA AATCAA A
73061 TTCGAATAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
5 5 0.09
6 41 0.73
7 10 0.18
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.19
Consensus pattern (6 bp):
AATCAA
Done.