Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009874.1 Kokia drynarioides strain JFW-HI SEQ_124609, 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: 45719
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:224 original size:31 final size:32
Alignment explanation
Indices: 170--229 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
160 GCAGCCCAGT
170 GACTTAAAATAAAAACTTTTGAATAGTTCGAA
1 GACTTAAAATAAAAACTTTTGAATAGTTCGAA
* *
202 GACTT-AAATGAAAATTTTTGAATAGTTC
1 GACTTAAAATAAAAACTTTTGAATAGTTC
230 AGTGACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (32 bp):
GACTTAAAATAAAAACTTTTGAATAGTTCGAA
Found at i:14309 original size:96 final size:92
Alignment explanation
Indices: 14143--14347 Score: 275
Period size: 96 Copynumber: 2.2 Consensus size: 92
14133 TCATGTTGTT
* * * * **
14143 TTAATTTTTTCTTTATTCAATCAATTATTAAAAAAAAAAATTACCATAAAAATACTAAATTTAAT
1 TTAATTTATTATTTATTCAATCAATCATTAAAAAAAAAAATTACCATAAAAATAATAAATCCAAT
*
14208 CAATCATATTTAATAAAGTTGCTTAAA
66 CAATCATATTGAATAAAGTTGCTTAAA
* * *
14235 TTAATTTATTGTTTATTCAATCAATCATTTAAGAAAAAAATATTTATCATAAAAAATAATAAATC
1 TTAATTTATTATTTATTCAATCAATCA-TTAA-AAAAAAA-AATTACCAT-AAAAATAATAAATC
14300 CAATCAATCATATTGAATAAAGTTGCTTAAA
62 CAATCAATCATATTGAATAAAGTTGCTTAAA
*
14331 TTGATTTATTATTTATT
1 TTAATTTATTATTTATT
14348 AAATATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
92 24 0.24
93 4 0.04
94 7 0.07
95 7 0.07
96 56 0.57
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (92 bp):
TTAATTTATTATTTATTCAATCAATCATTAAAAAAAAAAATTACCATAAAAATAATAAATCCAAT
CAATCATATTGAATAAAGTTGCTTAAA
Found at i:14974 original size:2 final size:2
Alignment explanation
Indices: 14967--14991 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14957 TCAAGGTAAT
14967 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14992 TCTCTCATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19531 original size:17 final size:18
Alignment explanation
Indices: 19504--19539 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
19494 TTTTCGAGCC
19504 AAACAAGAAAGAACCAAA
1 AAACAAGAAAGAACCAAA
*
19522 AAAC-AGAAAGAATCAAA
1 AAACAAGAAAGAACCAAA
19539 A
1 A
19540 CGTTTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.72, C:0.14, G:0.11, T:0.03
Consensus pattern (18 bp):
AAACAAGAAAGAACCAAA
Found at i:23907 original size:19 final size:19
Alignment explanation
Indices: 23883--23940 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
23873 GCCAACGAAT
23883 TATTTAAAATTTATAAAAA
1 TATTTAAAATTTATAAAAA
**
23902 TATTTAAAAAATATAAAAA
1 TATTTAAAATTTATAAAAA
*
23921 -ATTTCAAAATTCATAAAAA
1 TATTT-AAAATTTATAAAAA
23940 T
1 T
23941 TATAGAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTTAAAATTTATAAAAA
Found at i:24374 original size:31 final size:31
Alignment explanation
Indices: 24338--24402 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
24328 TATTTTTGTC
* *
24338 AATAAAAATATTGATTAAAGCAATAATTTTT
1 AATAAAAATATTGACTAAAACAATAATTTTT
24369 AATAAAAATATTGACTAAAACAATAATTTTT
1 AATAAAAATATTGACTAAAACAATAATTTTT
24400 AAT
1 AAT
24403 GTTATTGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (31 bp):
AATAAAAATATTGACTAAAACAATAATTTTT
Found at i:31506 original size:18 final size:20
Alignment explanation
Indices: 31480--31516 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
31470 ACAAAGGAAA
*
31480 AGAATGAAACAGAG-ATTAG
1 AGAATGAAAAAGAGCATTAG
31499 AGAA-GAAAAAGAGCATTA
1 AGAATGAAAAAGAGCATTA
31517 CAGGCCAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (20 bp):
AGAATGAAAAAGAGCATTAG
Found at i:36138 original size:23 final size:23
Alignment explanation
Indices: 36112--36155 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
36102 ATGAAAGTTG
*
36112 ATAGAATATAATTTAGGCTAACC
1 ATAGAATATAATGTAGGCTAACC
36135 ATAGAATATAATGTAGGCTAA
1 ATAGAATATAATGTAGGCTAA
36156 TATACAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (23 bp):
ATAGAATATAATGTAGGCTAACC
Found at i:39186 original size:22 final size:24
Alignment explanation
Indices: 39161--39212 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
39151 ATATATTTAA
39161 AAATAATAT-A-TTATAAA-TAATT
1 AAATAATATGATTTA-AAACTAATT
39183 AAAT-ATATGATTTAAAACTAATT
1 AAATAATATGATTTAAAACTAATT
39206 -AATAATA
1 AAATAATA
39213 ATAACACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 4 0.15
22 11 0.42
23 11 0.42
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATAATATGATTTAAAACTAATT
Found at i:40354 original size:2 final size:2
Alignment explanation
Indices: 40347--40373 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40337 AAATATTGAT
40347 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40374 TGGTGTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43210 original size:14 final size:15
Alignment explanation
Indices: 43193--43221 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43183 GAATTATTAT
43193 AAAGTCC-AATTACA
1 AAAGTCCAAATTACA
43207 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
43222 TGTTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Found at i:43952 original size:3 final size:3
Alignment explanation
Indices: 43946--43981 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
43936 TAATTGTTTT
43946 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43982 CATTTATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45185 original size:86 final size:89
Alignment explanation
Indices: 45032--45271 Score: 319
Period size: 86 Copynumber: 2.7 Consensus size: 89
45022 AGAGGTTCCT
* *
45032 AAACTATCCAAAAATTACATTTTTACCCCCGAACTTCAAAAAATTCCATTTTCGATCTCGAAACT
1 AAACT-TCCAAAAATTACATTTTTACCCCCAAACTTCAAAAAATTCCATTTTCGACCTCGAAACT
45097 TCCAAAAATTCCATTTTT-A-CCC-
65 TCCAAAAATTCCATTTTTGACCCCG
* * ** *
45119 TAACTTTCAAAAATTACATTTTTACCCTTAAACTTCAAAAAATTCCATTTTTGACCTCGAAACTT
1 AAACTTCCAAAAATTACATTTTTACCCCCAAACTTCAAAAAATTCCATTTTCGACCTCGAAACTT
45184 CCAAAAATTCCATTTTTGACCCCG
66 CCAAAAATTCCATTTTTGACCCCG
* * * *
45208 AAACTTCCAAAAATTCCATTTTTACTCCCGAA-TGTCCAAAAACTT-CATTTTCGACCTCGAAAC
1 AAACTTCCAAAAATTACATTTTTACCCCCAAACT-T-CAAAAAATTCCATTTTCGACCTCGAAAC
45271 T
64 T
45272 CTCAAAATTA
Statistics
Matches: 132, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
86 71 0.54
87 5 0.04
88 4 0.03
89 44 0.33
90 8 0.06
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (89 bp):
AAACTTCCAAAAATTACATTTTTACCCCCAAACTTCAAAAAATTCCATTTTCGACCTCGAAACTT
CCAAAAATTCCATTTTTGACCCCG
Found at i:45246 original size:59 final size:58
Alignment explanation
Indices: 45032--45318 Score: 264
Period size: 59 Copynumber: 4.9 Consensus size: 58
45022 AGAGGTTCCT
* * * * *
45032 AAACTATCCAAAAATTACATTTTTACCCCCGAACTTCAAAAAATTCCATTTTCGATCTCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
* * * **
45092 AAACTTCCAAAAATTCCATTTTTA-CCCTAACTTTCAAAAATTACATTTTT-ACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
* *
45148 AAACTTCAAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTGACCCCG
* *
45208 AAACTTCCAAAAATTCCATTTTTACTCCCGAA-TGTCCAAAAACTT-CATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTTTAC-CCCGAACT-TCCAAAAA-TTCCATTTTTGACCCCG
* * **
45267 AAAC-TCTC-AAAATTACC-CTTTTACCCCCGAATGTTTAAAAAATTCCATTTTT
1 AAACTTC-CAAAAATT-CCATTTTTA-CCCCGAA-CTTCCAAAAATTCCATTTTT
45319 AATCCTGAAC
Statistics
Matches: 189, Mismatches: 25, Indels: 27
0.78 0.10 0.11
Matches are distributed among these distances:
56 24 0.13
57 22 0.12
58 24 0.13
59 82 0.43
60 37 0.20
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:45319 original size:30 final size:29
Alignment explanation
Indices: 45032--45319 Score: 214
Period size: 30 Copynumber: 9.8 Consensus size: 29
45022 AGAGGTTCCT
* *
45032 AAACTATCCAAAAATTACATTTTTACCCCCG
1 AAACT-TCAAAAAATTCCATTTTTA-CCCCG
* * *
45063 -AACTTCAAAAAATTCCATTTTCGATCTCG
1 AAACTTCAAAAAATTCCATTTT-TACCCCG
*
45092 AAACTTCCAAAAATTCCATTTTTA-CCC-
1 AAACTTCAAAAAATTCCATTTTTACCCCG
* * **
45119 TAACTTTC-AAAAATTACATTTTTACCCTT
1 AAAC-TTCAAAAAATTCCATTTTTACCCCG
*
45148 AAACTTCAAAAAATTCCATTTTTGACCTCG
1 AAACTTCAAAAAATTCCATTTTT-ACCCCG
*
45178 AAACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCAAAAAATTCCATTTTT-ACCCCG
*
45208 AAACTTCCAAAAATTCCATTTTTACTCCCG
1 AAACTTCAAAAAATTCCATTTTTAC-CCCG
** * * * *
45238 AATGTCCAAAAACTT-CATTTTCGACCTCG
1 AAACTTCAAAAAATTCCATTTT-TACCCCG
*
45267 AAACTCTC--AAAATTACC-CTTTTACCCCCG
1 AAACT-TCAAAAAATT-CCATTTTTA-CCCCG
** *
45296 AATGTTTAAAAAATTCCATTTTTA
1 AAACTTCAAAAAATTCCATTTTTA
45320 ATCCTGAACT
Statistics
Matches: 205, Mismatches: 36, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
27 18 0.09
28 17 0.08
29 62 0.30
30 108 0.53
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
AAACTTCAAAAAATTCCATTTTTACCCCG
Found at i:45366 original size:88 final size:87
Alignment explanation
Indices: 45216--45382 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 87
45206 CGAAACTTCC
* *
45216 AAAAATTCCATTTTTACTCCCGAATGTCCAAAAACTTCATTTTCGACCTCGAAACTCTCAAAATT
1 AAAAATTCCATTTTTAATCCCGAATGTCCAAAAAC-TCATTTTCGACCTCGAAAATCTCAAAATT
*
45281 ACCCTTTTACCCCCGAATGTTTA
65 ACCATTTTACCCCCGAATGTTTA
* * *
45304 AAAAATTCCATTTTTAATCCTGAACTTTCACAAAATTAC-CATTTT-GCCCTCGAAAATC-CAAA
1 AAAAATTCCATTTTTAATCCCGAA-TGTC-CAAAA--ACTCATTTTCGACCTCGAAAATCTCAAA
*
45366 ATTACCATTTTTCCCCC
62 ATTACCATTTTACCCCC
45383 CCGGGTATCC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
88 41 0.60
89 14 0.21
90 11 0.16
92 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (87 bp):
AAAAATTCCATTTTTAATCCCGAATGTCCAAAAACTCATTTTCGACCTCGAAAATCTCAAAATTA
CCATTTTACCCCCGAATGTTTA
Done.