Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011538.1 Kokia drynarioides strain JFW-HI SEQ_126524, 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: 9061
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2345 original size:140 final size:139
Alignment explanation
Indices: 2138--2670 Score: 931
Period size: 140 Copynumber: 3.8 Consensus size: 139
2128 ACAAAACAGC
2138 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTT
1 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTT
* * *
2203 CCAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAGGCAGATTGA
66 CCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTGA
2268 AACAGTGAT
131 AACAGTGAT
* * *
2277 GGAATCATCTTCCTGATAATACACTGAGAAGAAGACCCAAAACGAGGCTCGAAACGAGCAAATCT
1 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCC-AAACGAGGCTCGAAACGAGCAAATCT
* * *
2342 TCCAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTG
65 TCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTG
2407 AAACAGTGAT
130 AAACAGTGAT
2417 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAACGAGGCTCGAAACGAGCAAATCT
1 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCC-AAACGAGGCTCGAAACGAGCAAATCT
* *
2482 TCCAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG
65 TCCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTG
2547 AAACAGTGAT
130 AAACAGTGAT
*
2557 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAGATCTT
1 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTT
*
2622 CCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATAAGATA
66 CCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATA
2671 AGCGAATTGA
Statistics
Matches: 376, Mismatches: 17, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
139 107 0.28
140 269 0.72
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (139 bp):
GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTT
CCAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAGAAGCGGATTGA
AACAGTGAT
Found at i:2761 original size:139 final size:135
Alignment explanation
Indices: 2139--2731 Score: 718
Period size: 140 Copynumber: 4.3 Consensus size: 135
2129 CAAAACAGCG
2139 GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTC
1 GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTC
* * * * *
2204 CAGATGAGGTACTAAGAAGTGAACCAAATTCGTCTTCCTGATAAGATACAGAG-A-GGCAGATTG
66 CAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTAATAAGATA-AGCGAATTG-AGA-T-
*
2267 AAAC-AGTGAT
127 AGACGA-TG-T
* *
2277 GGAATCATCTTCCTGATAATACACTGAGAAGAAGACCCAAAACGAGGCTCGAAACGAGCAAATCT
1 GG-ATCATCTTCCTGATGAGACACTGAGAAGAAGACCC-AAACGAGGCTCGAAACGAGCAAATCT
* * * *
2342 TCCAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTGATGAGATACAGAGAAGTG-GATT
64 TCCAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTAATAAGATA-AGCGAATTGAGA-T
*
2406 GAAAC-AGTGAT
127 -AGACGA-TG-T
2417 GGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAACGAGGCTCGAAACGAGCAAATCT
1 -GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCC-AAACGAGGCTCGAAACGAGCAAATCT
* *
2482 TCCAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG
64 TCCAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCC---T-A-ATA-AGATAAGCGAATTG
* * *
2547 AAACAG-TGATG-
123 AGATAGACGATGT
*
2558 GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAGATCTTC
1 GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTC
*
2623 CAGATGAGGTACTGAGAAGTGAACCAAATTCGTCTTCCTAATAAGATAAGCGAATTGAGATAGAC
66 CAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTAATAAGATAAGCGAATTGAGATAGAC
*
2688 GACGT
131 GATGT
** *
2693 GG-TCATCTTCCTGATGAGGTACTAAGAAGAAGA-CCAAAC
1 GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAAC
2732 CAAACCCACG
Statistics
Matches: 411, Mismatches: 29, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
133 22 0.05
134 34 0.08
135 3 0.01
136 1 0.00
138 2 0.00
139 97 0.24
140 230 0.56
141 3 0.01
142 1 0.00
143 3 0.01
144 2 0.00
145 8 0.02
146 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (135 bp):
GGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTCGAAACGAGCAAATCTTC
CAGATGAGGTACTGAGAAGTGAACTAAATTCGTCTTCCTAATAAGATAAGCGAATTGAGATAGAC
GATGT
Found at i:3203 original size:6 final size:6
Alignment explanation
Indices: 3192--3242 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
3182 AATTGAATTT
* * * *
3192 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTTAT A-TGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
3238 ATTTA
1 ATTTA
3243 TTATAAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
5 7 0.19
6 29 0.81
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:3215 original size:17 final size:17
Alignment explanation
Indices: 3187--3259 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
3177 TTGGTAATTG
3187 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
3203 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
3220 AATTTATATGAAATTTA
1 AATTTATTTTAAATTTA
*
3237 AATTTATTATAAGA-TTA
1 AATTTATTTTAA-ATTTA
3254 AATTTA
1 AATTTA
3260 GAGAGTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
16 5 0.10
17 42 0.88
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:4548 original size:118 final size:118
Alignment explanation
Indices: 4332--4862 Score: 753
Period size: 118 Copynumber: 4.5 Consensus size: 118
4322 CCCCAAAGGT
* * * * *
4332 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCGA
4397 ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG
66 ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG
* *
4450 CCCCAAAACTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCAA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCGA
* **
4515 ACCTTTTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAG
66 ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG
* * * ** *
4568 CCCCGAACCTTCCAAAAATTTCCATTCAACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCGA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCGA
*
4633 ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTTAG
66 ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG
* *
4686 CCCTAAACCTTCTAAAAATTACCATTTTACCC-CTGAACTTCTAAAAATCCCATTTTTGACCTCG
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCTC-GAACTTCTAAAAATCCCATTTTTGACCCCG
* * * *
4750 AATCTTCCAAAAATTACCGTTTTACCCCCGAACTCCCAAAAATCCCATTTTT-G
65 AACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG
* ** * * *
4803 ACCTCGGATCTTCTAAAAATAACCATTTTACCCTCGAACTTCCT-AAAATCCTATTTTTGA
1 -CCCCAAACCTTCTAAAAATTACCATTTTACCCTCGAACTT-CTAAAAATCCCATTTTTGA
4863 TTCCGGACAT
Statistics
Matches: 369, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
117 2 0.01
118 364 0.99
119 3 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (118 bp):
CCCCAAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCGA
ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAG
Found at i:4646 original size:177 final size:178
Alignment explanation
Indices: 4332--4862 Score: 750
Period size: 177 Copynumber: 3.0 Consensus size: 178
4322 CCCCAAAGGT
* * *
4332 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCGA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAGCCCCGA
* * *
4397 ACCTTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-AGCCCCAAAACTT
66 ACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACTT
4461 CTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGA-
130 CTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGAG
*
4509 CCCCAAACCTTTTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAGCCCCGA
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAGCCCCGA
* ** * * *
4574 ACCTTCCAAAAATTTCCATTCAACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCGAACCTT-
66 ACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTC
* *
4638 TCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTT-AG
131 T-AAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGAG
* * * *
4686 CCCTAAACCTTCTAAAAATTACCATTTTACCCCTGAACTTCTAAAAATCCCATTTTT-GACCTCG
1 CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAG-CCCCG
* * * * *
4750 AATCTTCCAAAAATTACCGTTTTACCCCCGAACTCCCAAAAATCCCATTTTTGACCTCGGATCTT
65 AACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTT
* *
4815 CTAAAAATAACCATTTTACCCTCGAACTTCCT-AAAATCCTATTTTTGA
130 CTAAAAATTACCATTTTACCCTCGAACTT-CTAAAAATCCCATTTTTGA
4863 TTCCGGACAT
Statistics
Matches: 313, Mismatches: 34, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
176 3 0.01
177 306 0.98
178 4 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (178 bp):
CCCCAAACCTTCTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAGCCCCGA
ACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTC
TAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGAG
Found at i:4861 original size:59 final size:59
Alignment explanation
Indices: 4332--4862 Score: 676
Period size: 59 Copynumber: 9.0 Consensus size: 59
4322 CCCCAAAGGT
* *
4332 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
4391 CCCCGAACCTT-TCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTT-A
1 CCCCGAACCTTCT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * *
4449 GCCCCAAAACTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * **
4509 CCCCAAACCTTTTAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTT-A
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * ** * *
4567 GCCCCGAACCTTCCAAAAATTTCCATTCAACCCTCGAACTTCTAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
4627 CCTCGAACCTT-TCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTT-A
1 CCCCGAACCTTCT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
** * *
4685 GCCCTAAACCTTCTAAAAATTACCATTTTACCCCTGAACTTCTAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * *
4745 CCTCGAATCTTCCAAAAATTACCGTTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * *
4804 CCTCGGATCTTCTAAAAATAACCATTTTACCCTCGAACTTCCTAAAATCCTATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
4863 TTCCGGACAT
Statistics
Matches: 412, Mismatches: 50, Indels: 20
0.85 0.10 0.04
Matches are distributed among these distances:
58 4 0.01
59 403 0.98
60 5 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:7828 original size:13 final size:13
Alignment explanation
Indices: 7810--7835 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7800 TAGATATATT
7810 ATTAAACTAGCAG
1 ATTAAACTAGCAG
7823 ATTAAACTAGCAG
1 ATTAAACTAGCAG
7836 TGCATACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTAAACTAGCAG
Done.