Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012305.1 Kokia drynarioides strain JFW-HI SEQ_127306, 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: 10453
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Warning! 79 characters in sequence are not A, C, G, or T
Found at i:1058 original size:29 final size:29
Alignment explanation
Indices: 1016--1442 Score: 437
Period size: 29 Copynumber: 14.6 Consensus size: 29
1006 CCCTAAATTG
1016 TCCAAAAATTCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* *
1045 TCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
* * *
1075 TCCAAAAATTTCA-TTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* *
1103 TCCAAGAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
* * *
1133 TTCAAAAATTCCATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * *
1162 TCCAAAAATTTCATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
*
1191 TCCAAAAA-TCCTATTTTTGACCCCGAAACT
1 TCCAAAAATTCC-ATTTTT-ACCCCCAAACT
*
1221 TCCAAAAATCCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* ***
1250 TCCAAAAATTCTATTTTTGACCTTGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
* * **
1280 TCCAAAATTTCCATTTTTA-CTCCTGACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * *
1308 TCCACAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
* *
1338 TCCAAAAATTACATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * * *
1367 TCCAAAAATCCCTTTTTTACTCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * * *
1396 TCCAAAAATTCCTTTTTTGTCCCCCGAACG
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
*
1426 TCCAAAAACTCCATTTT
1 TCCAAAAATTCCATTTT
1443 CGACCTCAAA
Statistics
Matches: 330, Mismatches: 58, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
28 41 0.12
29 153 0.46
30 134 0.41
31 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCCAAACT
Found at i:1178 original size:59 final size:57
Alignment explanation
Indices: 1016--1442 Score: 437
Period size: 59 Copynumber: 7.3 Consensus size: 57
1006 CCCTAAATTG
* * *
1016 TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTT-ACCCCCAAACT
* * *
1075 TCCAAAAATTTCA-TTTTACCCTCGAACTTCCAAGAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCATTTTT-ACCCCCAAACT
* * * *
1133 TTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTTCATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATTCCATTTTTACCCCCAAACT
*
1191 TCCAAAAA-TCCTATTTTTGACCCCGAAACTTCCAAAAATCCCATTTTTACCCCCAAACT
1 TCCAAAAATTCC-ATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTACCCCCAAACT
* ** * * **
1250 TCCAAAAATTCTATTTTTGACCTTGAAACTTCCAAAATTTCCATTTTTA-CTCCTGACT
1 TCCAAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTACCCCCAAACT
* * * * *
1308 TCCACAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTT-ACCCC-GAACTTCCAAAAATTCCATTTTTACCCCCAAACT
* * * * * *
1367 TCCAAAAATCCCTTTTTTACTCCCGAACTTCCAAAAATTCCTTTTTTGTCCCCCGAACG
1 TCCAAAAATTCCATTTTTAC-CCCGAACTTCCAAAAATTCCATTTTT-ACCCCCAAACT
*
1426 TCCAAAAACTCCATTTT
1 TCCAAAAATTCCATTTT
1443 CGACCTCAAA
Statistics
Matches: 312, Mismatches: 46, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
57 6 0.02
58 139 0.45
59 165 0.53
60 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCCCAAACT
Found at i:1183 original size:88 final size:85
Alignment explanation
Indices: 1020--1442 Score: 451
Period size: 88 Copynumber: 4.8 Consensus size: 85
1010 AAATTGTCCA
*
1020 AAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATT
1 AAAATTCCATTTTTA-CCCCAAACTTCCAAAAATCCCATTTTTGACCCC-AAACTTCCAAAAATT
1085 TCA-TTTTACCCTCGAACTTCC
64 TCATTTTTACCCTCGAACTTCC
* * *
1106 AAGAATTCCATTTTTGACCCCAAAACTTTCAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAA
1 AA-AATTCCATTTTT-ACCCC-AAACTTCCAAAAATCCCATTTTTGACCC-CAAACTTCCAAAAA
1170 TTTCATTTTTACCCTCGAACTTCC
62 TTTCATTTTTACCCTCGAACTTCC
*
1194 AAAAATCCTATTTTTGACCCCGAAACTTCCAAAAATCCCATTTTT-ACCCCCAAACTTCCAAAAA
1 AAAATTCC-ATTTTT-ACCCC-AAACTTCCAAAAATCCCATTTTTGA-CCCCAAACTTCCAAAAA
*
1258 -TTCTATTTTTGA-CCTTGAAACTTCC
62 TTTC-ATTTTT-ACCCTCG-AACTTCC
* ** *
1283 AAAATTTCCATTTTTACTCCTGACTTCCACAAATCCCATTTTTGACCCCAAAACTTCCAAAAATT
1 AAAA-TTCCATTTTTACCCCAAACTTCCAAAAATCCCATTTTTGACCCC-AAACTTCCAAAAATT
* *
1348 ACATTTTTACCCCCGAACTTCC
64 TCATTTTTACCCTCGAACTTCC
* * * * * * * * *
1370 AAAAATCCCTTTTTTACTCCCGAACTTCCAAAAATTCCTTTTTTGTCCCCCGAACGTCCAAAAAC
1 -AAAATTCCATTTTTAC-CCCAAACTTCCAAAAATCCCATTTTTG-ACCCCAAACTTCCAAAAAT
*
1435 TCCATTTT
63 TTCATTTT
1443 CGACCTCAAA
Statistics
Matches: 289, Mismatches: 30, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
86 2 0.01
87 87 0.30
88 170 0.59
89 27 0.09
90 3 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (85 bp):
AAAATTCCATTTTTACCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACTTCCAAAAATTTC
ATTTTTACCCTCGAACTTCC
Found at i:8028 original size:29 final size:30
Alignment explanation
Indices: 7985--8383 Score: 330
Period size: 29 Copynumber: 13.6 Consensus size: 30
7975 CCCTAAATTG
7985 TCCAAAAATTCCATTTTTACCCCT-GAACT
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
* * **
8014 TCAAAAAATCCCATTTTTGA-CCCTAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCTCGAACT
* *
8044 TCCAAAAATTTCATTTTTA-CTCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
* *
8073 TCCAAAAATTCCATTTTT-GCCCTCAAACT
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
* **
8102 TCCAAAAAATCCCATTTTTGACCCC-AAAACT
1 TCC-AAAAATTCCATTTTT-ACCCCTCGAACT
8133 TCCAAAACA-TCCATTTTTACCCCT-GAACT
1 TCCAAAA-ATTCCATTTTTACCCCTCGAACT
8162 TCCAAAAATTCCATTTTTA-CCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
* *
8191 TCCAAAAATCCCATTTTTA-CTCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
*
8220 T-CAACAAATCCCATTTTTGA--CCTCGAAACT
1 TCCAA-AAATTCCATTTTT-ACCCCTCG-AACT
8250 TCCAAAAATTCCATTTTTACCCC-CGAACT
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
** *** *
8279 TCCAAATTTTTTTTTTTTTACCCC-CAAACT
1 TCCAAA-AATTCCATTTTTACCCCTCGAACT
* *
8309 TCCAAAAA-TCCCTTTTTACTCC-CGAA-T
1 TCCAAAAATTCCATTTTTACCCCTCGAACT
* * * *
8336 CTCTAAAAACTCCATTTTTGTCCCC-CGAACG
1 -TCCAAAAATTCCATTTTT-ACCCCTCGAACT
* *
8367 TCTAAAAACTCCATTTT
1 TCCAAAAATTCCATTTT
8384 CGACCTCAAA
Statistics
Matches: 310, Mismatches: 39, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
27 1 0.00
28 28 0.09
29 151 0.49
30 113 0.36
31 14 0.05
32 3 0.01
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTACCCCTCGAACT
Found at i:8263 original size:88 final size:85
Alignment explanation
Indices: 7985--8393 Score: 387
Period size: 88 Copynumber: 4.7 Consensus size: 85
7975 CCCTAAATTG
* *
7985 TCCAAAAATTCCATTTTTACCC-CTGAACTTCAAAAAATCCCATTTTTGACCCTAAAACTTCCAA
1 TCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGA-CCTCAAACTTCCAA
*
8049 AAATTTCATTTTTACTCTCGAACT
64 AAA-TCCATTTTTAC-CTCGAACT
* * *
8073 TCCAAAAATTCCATTTTTGCCCTCAAACTTCCAAAAAATCCCATTTTTGACCCCAAAACTTCCAA
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCC-AAAAATCCCATTTTTGACCTC-AAACTTCCAA
*
8138 AACATCCATTTTTACCCCTGAACT
64 AA-ATCCATTTTTACCTC-GAACT
*
8162 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTT-ACTCTCGAACTT-CAAC
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC-CTCAAACTTCCAA-
8225 AAATCCCATTTTTGACCTCGAAACT
64 AAAT-CCATTTTT-ACCTCG-AACT
* ** **** * *
8250 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAATTTTTTTTTTTTTACCCCCAAACTTCCAAA
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-CCTCAAACTTCCAAA
* *
8315 AATCCCTTTTTACTCCCGAA-T
65 AATCCATTTTTAC-CTCGAACT
* * * * * * *
8336 CTCTAAAAACTCCATTTTTGTCCCCCGAACGTCTAAAAA-CTCCATTTTCGACCTCAAA
1 -TCCAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATC-CCATTTTTGACCTCAAA
8394 AATCTCAAAA
Statistics
Matches: 267, Mismatches: 37, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
86 6 0.02
87 44 0.16
88 125 0.47
89 87 0.33
90 5 0.02
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (85 bp):
TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCAAACTTCCAAAA
ATCCATTTTTACCTCGAACT
Found at i:8296 original size:59 final size:58
Alignment explanation
Indices: 7985--8354 Score: 331
Period size: 59 Copynumber: 6.3 Consensus size: 58
7975 CCCTAAATTG
* * * ***
7985 TCCAAAAATTCCATTTTTACCCCTG-AACTTCAAAAAATCCCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTTACCTC-GAAACTTCCAAAAATTCCATTTTT-ACCCCCGAACT
* * * *
8044 TCCAAAAATTTCATTTTTACTCTCG-AACTTCCAAAAATTCCATTTTTGCCCTCAAACT
1 TCCAAAAATTCCATTTTTAC-CTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACT
* * * *
8102 TCCAAAAAATCCCATTTTTGACCCCAAAACTTCCAAAACA-TCCATTTTTACCCCTGAACT
1 TCC-AAAAATTCCATTTTT-ACCTCGAAACTTCCAAAA-ATTCCATTTTTACCCCCGAACT
* * *
8162 TCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATCCCATTTTTACTCTCGAACT
1 TCCAAAAATTCCATTTTTA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACT
*
8220 T-CAACAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACT
1 TCCAA-AAATTCCATTTTT-ACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACT
** *** * * * *
8279 TCCAAATTTTTTTTTTTTTACCCCCAAACTTCCAAAAA-TCCCTTTTTACTCCCGAA-T
1 TCCAAA-AATTCCATTTTTACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACT
* *
8336 CTCTAAAAACTCCATTTTT
1 -TCCAAAAATTCCATTTTT
8355 GTCCCCCGAA
Statistics
Matches: 256, Mismatches: 42, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
57 11 0.04
58 79 0.31
59 122 0.48
60 43 0.17
61 1 0.00
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACT
Found at i:8355 original size:117 final size:117
Alignment explanation
Indices: 7990--8334 Score: 367
Period size: 118 Copynumber: 2.9 Consensus size: 117
7980 AATTGTCCAA
* ** * ***
7990 AAATTCCATTTTT-ACCCCTGAACTT-CAAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAAT
1 AAATCCCATTTTTGACCCCAAAACTTCCAAAACAT-CCATTTTT-ACCCCCGAACTTCCAAAAAT
* * * * * * * *
8053 TTCATTTTTACTCTCGAACTTCCAAAAATTCCATTTTTGC-CCTCAAACTTCCAAA
64 TCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACTCC-CGAACTT-CAAC
*
8108 AAATCCCATTTTTGACCCCAAAACTTCCAAAACATCCATTTTTACCCCTGAACTTCCAAAAATTC
1 AAATCCCATTTTTGACCCCAAAACTTCCAAAACATCCATTTTTACCCCCGAACTTCCAAAAATTC
* * *
8173 CATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTACTCTCGAACTTCAAC
66 CATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACTCCCGAACTTCAAC
* * **
8225 AAATCCCATTTTTGACCTCGAAACTTCCAAAA-ATTCCATTTTTACCCCCGAACTTCCAAATTTT
1 AAATCCCATTTTTGACCCCAAAACTTCCAAAACA-TCCATTTTTACCCCCGAACTTCCAAA-AAT
***
8289 TTTTTTTTTACCCCCAAACTTCCAAAAATCCC-TTTTTACTCCCGAA
64 TCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACTCCCGAA
8335 TCTCTAAAAA
Statistics
Matches: 197, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
116 1 0.01
117 71 0.36
118 99 0.50
119 19 0.10
120 7 0.04
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.34
Consensus pattern (117 bp):
AAATCCCATTTTTGACCCCAAAACTTCCAAAACATCCATTTTTACCCCCGAACTTCCAAAAATTC
CATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTACTCCCGAACTTCAAC
Found at i:9970 original size:6 final size:6
Alignment explanation
Indices: 9961--10007 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
9951 ATTTATCTTC
** *
9961 TTAAAT TTAAAT TT-GCT TTAAAT TTAAAT TT-AAT TAAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
10007 T
1 T
10008 GACTTAAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:9983 original size:17 final size:17
Alignment explanation
Indices: 9961--10007 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
9951 ATTTATCTTC
**
9961 TTAAATTTAAATTTGCT
1 TTAAATTTAAATTTAAT
9978 TTAAATTTAAATTTAAT
1 TTAAATTTAAATTTAAT
*
9995 TAAAATTTAAATT
1 TTAAATTTAAATT
10008 GACTTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTAAATTTAAATTTAAT
Found at i:10006 original size:34 final size:35
Alignment explanation
Indices: 9963--10034 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
9953 TTATCTTCTT
* * *
9963 AAATTTAAATTTG-CTTTAAATTTAA-ATTTAATTA
1 AAATTTAAA-TTGACTTAAAACTTAATATTAAATTA
9997 AAATTTAAATTGACTTAAAACTTAATATTAAATTA
1 AAATTTAAATTGACTTAAAACTTAATATTAAATTA
10032 AAA
1 AAA
10035 GTCCAAGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 3 0.09
34 19 0.58
35 11 0.33
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (35 bp):
AAATTTAAATTGACTTAAAACTTAATATTAAATTA
Found at i:10014 original size:17 final size:17
Alignment explanation
Indices: 9963--10021 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
9953 TTATCTTCTT
*
9963 AAATTTAAATTTG-CTTT
1 AAATTTAAA-TTGACTTA
* *
9980 AAATTTAAATTTAATTA
1 AAATTTAAATTGACTTA
9997 AAATTTAAATTGACTTA
1 AAATTTAAATTGACTTA
*
10014 AAACTTAA
1 AAATTTAA
10022 TATTAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 2 0.06
17 33 0.94
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTGACTTA
Found at i:10034 original size:18 final size:17
Alignment explanation
Indices: 9984--10034 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
9974 TGCTTTAAAT
* *
9984 TTAAATTTAATTAAAAT
1 TTAAATTAAATTAAAAC
* *
10001 TTAAATTGACTTAAAAC
1 TTAAATTAAATTAAAAC
10018 TTAATATTAAATTAAAA
1 TTAA-ATTAAATTAAAA
10035 GTCCAAGACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAAATTAAATTAAAAC
Done.