Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001303.1 Kokia drynarioides strain JFW-HI SEQ_112716, 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: 9114
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Found at i:592 original size:21 final size:21
Alignment explanation
Indices: 563--621 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
553 GTGTCTACAA
*
563 AAGTAAGACTTGTATCGGTAG
1 AAGTGAGACTTGTATCGGTAG
* *
584 AAGTGAGACTTGTTTTGGTAG
1 AAGTGAGACTTGTATCGGTAG
* *
605 AACTGACACTTGTATCG
1 AAGTGAGACTTGTATCG
622 ATAAAAAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (21 bp):
AAGTGAGACTTGTATCGGTAG
Found at i:1894 original size:52 final size:52
Alignment explanation
Indices: 1814--2052 Score: 309
Period size: 52 Copynumber: 4.6 Consensus size: 52
1804 TAAATGAAAA
* * *
1814 AGGTCCGATGACTATGTGTCATCTTGAGTATATGAATCATTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1866 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTA-GAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG-GATTATG
* * * *
1918 AGGTCCGATGACTGTGTGTTATTGTGAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * ** **
1970 AGGTTCAATGACTATGTGACATCGTGAGTATATGATTCCTTTACAAATTAAA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
2022 AGGTCTGATGACTATGTGCCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
2053 TAAATGAAAT
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
51 1 0.01
52 161 0.99
53 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:2760 original size:21 final size:22
Alignment explanation
Indices: 2731--2786 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
2721 GGAGTTTTTA
2731 GTATCGGTAGAAGTAAT-ACTT
1 GTATCGGTAGAAGTAATCACTT
* * *
2752 GTTTCGGTATAAG-AGTCACTT
1 GTATCGGTAGAAGTAATCACTT
2773 GTATCGGTAGAAGT
1 GTATCGGTAGAAGT
2787 CTACACTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (22 bp):
GTATCGGTAGAAGTAATCACTT
Found at i:3266 original size:265 final size:265
Alignment explanation
Indices: 2793--3274 Score: 698
Period size: 265 Copynumber: 1.8 Consensus size: 265
2783 AAGTCTACAC
* * * * *
2793 TATTCTTGAACTGTTTACTAACTTGACAACTACCGATACTTGTCCAACAATTACTGATAGAAGTT
1 TATTCTTAAACTGGTTACTAACTTGACAACTACCGATACTTGTCCAACAAGTACCGATAGAAGTC
* * *
2858 TCCAAAAATCTTAGAAGTGACCTTTTTGCCCTTGTTGAATTGTGATTATAATTAATAGATAATTT
66 TCCAAAAATCTTAGAAATGACCTTTTTGCCCTTGTTGAATAGTGATTATAACTAATAGATAATTT
* ** ** * * *
2923 TTGGCGTGTTAGGTGTATTTCTTTAAAAATGTAAGATTAAATGACATAATTTTAAAGATGAATAG
131 TTGACGTAATAGGTACATTTCTTTAAAAATATAAGATTAAATGACATAATTTAAAAGAAGAATAG
2988 TGATAGATGAATAGAGTGACACCGAGACTCTTGTCGGTGACGGTTTCTGAGTTTTGGGTGTTACA
196 TGATAGATGAATAGAGTGACACCGAGACTCTTGTCGGTGACGGTTTCTGAGTTTTGGGTGTTACA
3053 TGCAT
261 TGCAT
* * *
3058 TATTCTTAAACTGGTTATTGACTTGACAACTATCGATACTTGTCCAACAAGTACCGATAGAAGTC
1 TATTCTTAAACTGGTTACTAACTTGACAACTACCGATACTTGTCCAACAAGTACCGATAGAAGTC
* *
3123 TCCAAAAATCTT-GAAAATGACCTTTTTGCCCTTGTTGAATAGTGATTATAACTAATTGTTAATT
66 TCCAAAAATCTTAG-AAATGACCTTTTTGCCCTTGTTGAATAGTGATTATAACTAATAGATAATT
* * * *
3187 TTTGACGTAAT-GGCTACATTTCTTTGATAATATGAGATTAAATGACGTAATTTAAAAGAAGAAT
130 TTTGACGTAATAGG-TACATTTCTTTAAAAATATAAGATTAAATGACATAATTTAAAAGAAGAAT
*
3251 AGTGATTGATGAATAGAGTGACAC
194 AGTGATAGATGAATAGAGTGACAC
3275 TGGGGCCCTA
Statistics
Matches: 189, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
264 3 0.02
265 186 0.98
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (265 bp):
TATTCTTAAACTGGTTACTAACTTGACAACTACCGATACTTGTCCAACAAGTACCGATAGAAGTC
TCCAAAAATCTTAGAAATGACCTTTTTGCCCTTGTTGAATAGTGATTATAACTAATAGATAATTT
TTGACGTAATAGGTACATTTCTTTAAAAATATAAGATTAAATGACATAATTTAAAAGAAGAATAG
TGATAGATGAATAGAGTGACACCGAGACTCTTGTCGGTGACGGTTTCTGAGTTTTGGGTGTTACA
TGCAT
Found at i:3995 original size:59 final size:59
Alignment explanation
Indices: 3817--3998 Score: 195
Period size: 60 Copynumber: 3.1 Consensus size: 59
3807 TTAGGTACTG
* * * * *
3817 AATTGAATCTAAAAAAATTTTAGGTACCAAATT-AGAAAAAAATGCCAAGTTCAGGTACCA
1 AATTGAGTC-AAAAAAAATTTAGGTACCAAATTAAG-AAAAAGTGTCAAGTTAAGGTACCA
* * ** * * *
3877 AATTGGGTCCAAGAAAGGTTTAGGTACCAAATTAAAAAAAAGTATCAAGTTTAGGTACCA
1 AATTGAGT-CAAAAAAAATTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTAAGGTACCA
* * *
3937 AATTGAGTCAAAAAAAATTTAAGTACTAAATTAAGAAAAAGTGTCAAGTTAAGATACCA
1 AATTGAGTCAAAAAAAATTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTAAGGTACCA
3996 AAT
1 AAT
3999 GATACATTAA
Statistics
Matches: 100, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
59 45 0.45
60 53 0.53
61 2 0.02
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.25
Consensus pattern (59 bp):
AATTGAGTCAAAAAAAATTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTAAGGTACCA
Found at i:8283 original size:18 final size:18
Alignment explanation
Indices: 8260--8297 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
8250 ATTTAACAAG
8260 ATAGTGTCTAAAATAGAT
1 ATAGTGTCTAAAATAGAT
8278 ATAGTGTCTAAAATAGAT
1 ATAGTGTCTAAAATAGAT
8296 AT
1 AT
8298 TTCATGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (18 bp):
ATAGTGTCTAAAATAGAT
Found at i:8568 original size:21 final size:22
Alignment explanation
Indices: 8526--8568 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
8516 TTTATTTCAA
* **
8526 AAAGAGTAAAATTATTGGAATT
1 AAAGAGTAAAATAATTAAAATT
8548 AAAG-GTAAAATAATTAAAATT
1 AAAGAGTAAAATAATTAAAATT
8569 TAAAAGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (22 bp):
AAAGAGTAAAATAATTAAAATT
Done.