Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006419.1 Kokia drynarioides strain JFW-HI SEQ_121000, 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: 39951
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3262 original size:2 final size:2
Alignment explanation
Indices: 3255--3284 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3245 TTGATTAAAA
3255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3285 TTTACAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14422 original size:22 final size:22
Alignment explanation
Indices: 14394--14437 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
14384 CAGTAGATGA
14394 GTGAGCGTAACAATTCATCGGT
1 GTGAGCGTAACAATTCATCGGT
14416 GTGAGCGTAACAATTCATCGGT
1 GTGAGCGTAACAATTCATCGGT
14438 TAAAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (22 bp):
GTGAGCGTAACAATTCATCGGT
Found at i:16683 original size:5 final size:6
Alignment explanation
Indices: 16661--16693 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
16651 AGCTGTTTCT
16661 AAAAAG TAAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AA
16694 TGACAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:23089 original size:141 final size:142
Alignment explanation
Indices: 22803--23361 Score: 674
Period size: 141 Copynumber: 4.0 Consensus size: 142
22793 CTTTCCTAAC
* * * * * ** *
22803 ATAGATTCGTCCCATAA-GTCACTCCCTTGCTAGAGAAAAAACTTGTCCTTGAGCTTGGAGTTAG
1 ATAGATTCGGCCCATAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGTTAG
* * * *
22867 GATAAACTTGGTGAAAGGTCCCA--TCATTACTGATAGTCGAAACCGATAAGGGTTGTGGACCTA
66 GATAAACTTGGCGAAAGGTCCCATTTCATTACTAATAGTTGAAACCGATAGGGGTTGTGGACCTA
* *
22930 CGCAAACTTATA
131 CACAAACTTATT
*
22942 ATAGATTCGGCTCATAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGTTAG
1 ATAGATTCGGCCCATAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGTTAG
* * *
23007 GGTAAACTTGGCGAAA-GTCCCATTTCATTACTAATAGTTTAAACCGATTGGGGTTGTGGACCGT
66 GATAAACTTGGCGAAAGGTCCCATTTCATTACTAATAGTTGAAACCGATAGGGGTTGTGGACC-T
23071 -CACAAACTTATT
130 ACACAAACTTATT
* *
23083 ATAGATTCGGCCCTTAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGCTAG
1 ATAGATTCGGCCCATAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGTTAG
* **** *** **
23148 GATAAACTTGGAGAAAGGTCCCNCCCCCA-T--T-A-AGTTGAAATTTATAGGGGCCGTGGACCT
66 GATAAACTTGGCGAAAGGTCCC-ATTTCATTACTAATAGTTGAAACCGATAGGGGTTGTGGACCT
*
23208 ACACAAACTTGTT
130 ACACAAACTTATT
* *
23221 ATAGATTAGGCCCATAATATTACTCCCTTGCTAGAGAAAGACCTTGTCCTCAAGCTCGGAGTTAG
1 ATAGATTCGGCCCATAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGTTAG
* *
23286 GATAAACCTGGCGAAAGG-CCC-TTTCCATTACTAATAGTTGAAACTGATAGGGGTTGTGGACCT
66 GATAAACTTGGCGAAAGGTCCCATTT-CATTACTAATAGTTGAAACCGATAGGGGTTGTGGACCT
**
23349 ATGCAAACTTATT
130 ACACAAACTTATT
23362 CTTATTTATT
Statistics
Matches: 356, Mismatches: 51, Indels: 24
0.83 0.12 0.06
Matches are distributed among these distances:
136 2 0.01
137 5 0.01
138 108 0.30
139 23 0.06
140 56 0.16
141 153 0.43
142 7 0.02
143 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (142 bp):
ATAGATTCGGCCCATAATATTACTCCCTTGCTAGAGAAAGAGCTTGTCCTCAAGCTCGGAGTTAG
GATAAACTTGGCGAAAGGTCCCATTTCATTACTAATAGTTGAAACCGATAGGGGTTGTGGACCTA
CACAAACTTATT
Found at i:24724 original size:53 final size:53
Alignment explanation
Indices: 24644--24750 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
24634 TCGACACTTC
24644 TTTACAAGATGCTCCAAAATGCAGTAACCACAGCAAGAAAAAATATTTGAAGA
1 TTTACAAGATGCTCCAAAATGCAGTAACCACAGCAAGAAAAAATATTTGAAGA
24697 TTTACAAGATGCTCCAAAATGCAGTAACCACAGCAAGAAAAAATATTTGAAGA
1 TTTACAAGATGCTCCAAAATGCAGTAACCACAGCAAGAAAAAATATTTGAAGA
24750 T
1 T
24751 AACAAACCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (53 bp):
TTTACAAGATGCTCCAAAATGCAGTAACCACAGCAAGAAAAAATATTTGAAGA
Found at i:29934 original size:32 final size:30
Alignment explanation
Indices: 29889--29947 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
29879 CATTAATAAT
*
29889 TAAATAAATATTTAAAATATTCATAAAATTAA
1 TAAATAAAAATTTAAAA-ATT-ATAAAATTAA
29921 TAAATAAAAATTTAAAAATTATAAAAT
1 TAAATAAAAATTTAAAAATTATAAAAT
29948 CCATAACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.27
31 3 0.12
32 16 0.62
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAATAAAAATTTAAAAATTATAAAATTAA
Found at i:34117 original size:14 final size:14
Alignment explanation
Indices: 34098--34127 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
34088 AATTCTTTTT
34098 ACCTCGAATCTTGA
1 ACCTCGAATCTTGA
34112 ACCTCGAATCTTGA
1 ACCTCGAATCTTGA
34126 AC
1 AC
34128 TCTAAATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (14 bp):
ACCTCGAATCTTGA
Found at i:34286 original size:21 final size:21
Alignment explanation
Indices: 34260--34317 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
34250 ACCTTGAGTT
* *
34260 TTTAAGGTTTGAGGTTT-GAG
1 TTTAAGATTTGAGATTTCGAG
34280 ATTTAAGATTTGAGATTTCGAG
1 -TTTAAGATTTGAGATTTCGAG
*
34302 TTTAA-ATTTGAAATTT
1 TTTAAGATTTGAGATTT
34318 AAAGTTTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.30
21 20 0.61
22 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (21 bp):
TTTAAGATTTGAGATTTCGAG
Found at i:34323 original size:20 final size:21
Alignment explanation
Indices: 34281--34325 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
34271 AGGTTTGAGA
* **
34281 TTTAAGATTTGAGATTTCGAG
1 TTTAAGATTTGAAATTTAAAG
34302 TTTAA-ATTTGAAATTTAAAG
1 TTTAAGATTTGAAATTTAAAG
34322 TTTA
1 TTTA
34326 TGGATCAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (21 bp):
TTTAAGATTTGAAATTTAAAG
Done.