Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013740.1 Kokia drynarioides strain JFW-HI SEQ_128768, 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: 9008
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4566 original size:10 final size:10
Alignment explanation
Indices: 4553--4600 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
4543 CAAAGAGTTT
4553 TTAATATATA
1 TTAATATATA
4563 TTAATATAT-
1 TTAATATATA
*
4572 TTAATATTTA
1 TTAATATATA
*
4582 TTTATTATATA
1 -TTAATATATA
4593 TTAATATA
1 TTAATATA
4601 CTTATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATATATA
Found at i:4576 original size:19 final size:20
Alignment explanation
Indices: 4552--4600 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
4542 TCAAAGAGTT
4552 TTTAATATATA-TTAATATA
1 TTTAATATATATTTAATATA
* *
4571 TTTAATATTTATTTATTATA
1 TTTAATATATATTTAATATA
4591 TATTAATATA
1 T-TTAATATA
4601 CTTATTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 8 0.32
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATATATATTTAATATA
Found at i:4607 original size:19 final size:19
Alignment explanation
Indices: 4552--4607 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
4542 TCAAAGAGTT
4552 TTTAATATA-TATTAATATA
1 TTTAATATATTATT-ATATA
4571 TTTAATAT-TTATTTATTATA
1 TTTAATATATTA-TTA-TATA
4591 TATTAATATACTTATTA
1 T-TTAATATA-TTATTA
4608 ATTGCTATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 11 0.35
20 7 0.23
21 7 0.23
22 3 0.10
23 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATATATTATTATATA
Found at i:5059 original size:30 final size:30
Alignment explanation
Indices: 5023--5083 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
5013 ATTGCTCAGA
*
5023 GGTCCCTAAACTTTCTAA-AAATCATATTTT
1 GGTCCCTAAA-TTTCTAAGAAATCACATTTT
*
5053 GGTCCCTAAATTTTTAAGAAATCACATTTT
1 GGTCCCTAAATTTCTAAGAAATCACATTTT
5083 G
1 G
5084 ACCCTCGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (30 bp):
GGTCCCTAAATTTCTAAGAAATCACATTTT
Found at i:5305 original size:150 final size:148
Alignment explanation
Indices: 5071--5553 Score: 483
Period size: 150 Copynumber: 3.2 Consensus size: 148
5061 AATTTTTAAG
* ** * * * *
5071 AAATCACATTTTGACCCTCGAACTTTTCCAAAATTACATCTTGA-CCTCCGAACTTCTCTAAAAT
1 AAAT-ACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCT-AGAACTTCTCCAAAAT
* * *
5135 TACACTTTAGTCTCCGAACTCTTCCAAAATTGCATTTTGACCTCTAAGCTTTTCAAAAGTTACAT
64 TACACTTTAGCCTTCAAACTCTTCCAAAATTGCATTTTGACCTCTAA-CTTTTCAAAA-TTACAT
*
5200 TTTAACTCTTAAACTTTTCAAA
127 TTTAACCCTTAAACTTTTCAAA
*
5222 AAATACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAGAACATCTCCAAAATTA
1 AAATACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAGAACTTCTCCAAAATTA
*
5287 CACTTTAGCCTTTAAACTCTTCCAAAATTGCATTTTGACC-CTTAAACTTTTCCAAAATTACATT
66 CACTTTAGCCTTCAAACTCTTCCAAAATTGCATTTTGACCTC-T-AACTTTT-CAAAATTACATT
*
5351 TTAACCCCTTAACCTTTTCAAA
128 TTAA-CCCTTAAACTTTTCAAA
* * * * * *
5373 AATTACATTTTGACCCCTTAACCTTTTCCAAAATTACATTTTGACCCCTTA-ACCTTTTCCAAAA
1 AAATACATTTT-AACCCTTAAACTTTTCCAAAATTACATTTT-AACCC-TAGAACTTCTCCAAAA
* * * * ** * * *
5437 TTATA-TTTTGACAC-TCACACT-TTCCCAAATCACATTTTGACCTCGAACTTTCCTAAAATCAC
63 TTACACTTTAG-C-CTTCAAACTCTTCCAAAATTGCATTTTGACCTCTAACTTTTC-AAAATTAC
* * *
5499 ATTTTGACCCCTAAACTTTTCCAA
125 ATTTTAACCCTTAAACTTTTCAAA
* * *
5523 AATTACATTTTTACCCTTAAACTTTTGCAAA
1 AAATACATTTTAACCCTTAAACTTTTCCAAA
5554 GTTTTGCAAA
Statistics
Matches: 281, Mismatches: 39, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
149 17 0.06
150 128 0.46
151 58 0.21
152 50 0.18
153 25 0.09
154 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (148 bp):
AAATACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAGAACTTCTCCAAAATTA
CACTTTAGCCTTCAAACTCTTCCAAAATTGCATTTTGACCTCTAACTTTTCAAAATTACATTTTA
ACCCTTAAACTTTTCAAA
Found at i:5368 original size:31 final size:30
Alignment explanation
Indices: 5071--5553 Score: 410
Period size: 30 Copynumber: 16.1 Consensus size: 30
5061 AATTTTTAAG
* **
5071 AAATCACATTTTGACCCTCGAACTTTTCCA
1 AAATTACATTTTGACCCTTAAACTTTTCCA
* ** * *
5101 AAATTACATCTTGA-CCTCCGAACTTCTCTA
1 AAATTACATTTTGACCCT-TAAACTTTTCCA
* * * *
5131 AAATTACACTTTAGTCTCC--GAACTCTTCCA
1 AAATTACA-TTTTGAC-CCTTAAACTTTTCCA
* *
5161 AAATTGCATTTTGA-CCTCTAAGCTTTT-CA
1 AAATTACATTTTGACCCT-TAAACTTTTCCA
* * *
5190 AAAGTTACATTTTAACTCTTAAACTTTTCAA
1 AAA-TTACATTTTGACCCTTAAACTTTTCCA
* *
5221 AAAATACATTTTAACCCTTAAACTTTTCCA
1 AAATTACATTTTGACCCTTAAACTTTTCCA
* * *
5251 AAATTACATTTTAACCC-TAGAACATCTCCA
1 AAATTACATTTTGACCCTTA-AACTTTTCCA
* * *
5281 AAATTACACTTT-AGCCTTTAAACTCTTCCA
1 AAATTACATTTTGA-CCCTTAAACTTTTCCA
*
5311 AAATTGCATTTTGACCCTTAAACTTTTCCA
1 AAATTACATTTTGACCCTTAAACTTTTCCA
* * *
5341 AAATTACATTTTAACCCCTTAACCTTTTCAA
1 AAATTACATTTTGA-CCCTTAAACTTTTCCA
*
5372 AAATTACATTTTGACCCCTTAACCTTTTCCA
1 AAATTACATTTTGA-CCCTTAAACTTTTCCA
*
5403 AAATTACATTTTGACCCCTTAACCTTTTCCA
1 AAATTACATTTTGA-CCCTTAAACTTTTCCA
* * * * *
5434 AAATTATATTTTGACACTCACAC-TTTCCC
1 AAATTACATTTTGACCCTTAAACTTTTCCA
* **
5463 AAATCACATTTTGA-CCTCGAAC-TTTCCTA
1 AAATTACATTTTGACCCTTAAACTTTTCC-A
* *
5492 AAATCACATTTTGACCCCTAAACTTTTCCA
1 AAATTACATTTTGACCCTTAAACTTTTCCA
* *
5522 AAATTACATTTTTACCCTTAAACTTTTGCA
1 AAATTACATTTTGACCCTTAAACTTTTCCA
5552 AA
1 AA
5554 GTTTTGCAAA
Statistics
Matches: 374, Mismatches: 61, Indels: 36
0.79 0.13 0.08
Matches are distributed among these distances:
27 2 0.01
28 10 0.03
29 46 0.12
30 210 0.56
31 104 0.28
33 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATTACATTTTGACCCTTAAACTTTTCCA
Found at i:5473 original size:29 final size:29
Alignment explanation
Indices: 5428--5533 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 29
5418 CCCTTAACCT
* *
5428 TTTCC-AAAATTATATTTTGACACTC-ACAC
1 TTTCCTAAAATCACATTTTGAC-CTCGA-AC
*
5457 TTTCC-CAAATCACATTTTGACCTCGAAC
1 TTTCCTAAAATCACATTTTGACCTCGAAC
* *
5485 TTTCCTAAAATCACATTTTGACCCCTAAAC
1 TTTCCTAAAATCACATTTTGACCTC-GAAC
*
5515 TTTTCC-AAAATTACATTTT
1 -TTTCCTAAAATCACATTTT
5534 TACCCTTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 10 0.15
29 36 0.55
30 15 0.23
31 5 0.08
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTCCTAAAATCACATTTTGACCTCGAAC
Done.