Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011608.1 Kokia drynarioides strain JFW-HI SEQ_126598, 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: 25331
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1163 original size:17 final size:18
Alignment explanation
Indices: 1131--1167 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1121 GTTGATTGTG
*
1131 TTTAATTGCTTGTTTATA
1 TTTAATTGCATGTTTATA
1149 TTTAATT-CATGTTTATA
1 TTTAATTGCATGTTTATA
1166 TT
1 TT
1168 GTTATAGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (18 bp):
TTTAATTGCATGTTTATA
Found at i:9507 original size:18 final size:18
Alignment explanation
Indices: 9486--9524 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9476 AAGAAGATCT
* *
9486 AGAAGAGGATATTGAGGA
1 AGAAGAAGATACTGAGGA
*
9504 AGAAGAAGATCCTGAGGA
1 AGAAGAAGATACTGAGGA
9522 AGA
1 AGA
9525 TCCTGTGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.36, T:0.13
Consensus pattern (18 bp):
AGAAGAAGATACTGAGGA
Found at i:10188 original size:49 final size:50
Alignment explanation
Indices: 10110--10416 Score: 241
Period size: 50 Copynumber: 6.2 Consensus size: 50
10100 AAAATACGAT
* * *
10110 CCTTTCCCATCACATATTCTTAGGTACCGGGTTCGTCGTTGCGGCCTCAA
1 CCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAA
*** * * * *
10160 CCTTTCCCTTTGTATCTTCGT-GGTACCGGGTTCACCATTACGGCCTCAA
1 CCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAA
* ** * * * *
10209 CCTTTCCCATT-GCATCTTCTTAGGTATTGGATTTGCCGTCGCGGCCTTAA
1 CCTTTCCC-TTCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAA
* * * *
10259 -TTCTTCCCTTCATC-TCTTCAT-GGTATCGGGTTCGCCGTTGCAGCCTCAA
1 CCT-TTCCCTTCA-CATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAA
* * ** * *
10308 CCTTTCTCTTCACATCTTCTTAGGCACCAAGTTCACCGTTACGGCCTCAA
1 CCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAA
* ** *
10358 CCTTTCCCTTCACATCTT-TTAAGGTATCGAATTCACCGTTGCGGCCTCAA
1 CCTTTCCCTTCACATCTTCTT-AGGTACCGGGTTCGCCGTTGCGGCCTCAA
10408 TCC-TTCCCT
1 -CCTTTCCCT
10417 GTCAAACCTA
Statistics
Matches: 201, Mismatches: 46, Indels: 20
0.75 0.17 0.07
Matches are distributed among these distances:
48 1 0.00
49 81 0.40
50 116 0.58
51 3 0.01
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.35
Consensus pattern (50 bp):
CCTTTCCCTTCACATCTTCTTAGGTACCGGGTTCGCCGTTGCGGCCTCAA
Found at i:10608 original size:40 final size:42
Alignment explanation
Indices: 10510--10617 Score: 112
Period size: 40 Copynumber: 2.6 Consensus size: 42
10500 TTAACTAAAT
*
10510 GCCCTTTACGGGTTTTCAACTCAAAATTCTTTTGGTTTCAAGAC
1 GCCCTTTACGGGTTTTCATCTC-AAATTCTTTT-GTTTCAAGAC
* * * * ** *
10554 GGCTTTTGCAGGTTTTCATCTC-GGTTCTTTT-TTTCGAGAC
1 GCCCTTTACGGGTTTTCATCTCAAATTCTTTTGTTTCAAGAC
10594 GCCCTTTACGGGTTTTCATCTCAA
1 GCCCTTTACGGGTTTTCATCTCAA
10618 TTTTAGGCAA
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
40 26 0.52
42 7 0.14
44 17 0.34
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (42 bp):
GCCCTTTACGGGTTTTCATCTCAAATTCTTTTGTTTCAAGAC
Found at i:15858 original size:56 final size:56
Alignment explanation
Indices: 15791--15901 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
15781 TTATTTGATG
15791 TACACATTTAGGTAGGAAAATCGAATTTCGTAATGATTGAGAAAGAAAGTTACGTT
1 TACACATTTAGGTAGGAAAATCGAATTTCGTAATGATTGAGAAAGAAAGTTACGTT
15847 TACACATTTAGGTAGGAAAATCGAATTTCGTAATGATTGAGAAAGAAAGTTACGT
1 TACACATTTAGGTAGGAAAATCGAATTTCGTAATGATTGAGAAAGAAAGTTACGT
15902 CTAGTGAGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.30
Consensus pattern (56 bp):
TACACATTTAGGTAGGAAAATCGAATTTCGTAATGATTGAGAAAGAAAGTTACGTT
Found at i:16421 original size:30 final size:30
Alignment explanation
Indices: 16374--16575 Score: 189
Period size: 30 Copynumber: 6.9 Consensus size: 30
16364 AGTTTCGAAG
* * *
16374 AGTTTG-GGGTCAAAATGTGATTTTTAAAA
1 AGTTTGAGGGTAAAAATGTGATTTTTGAGA
*
16403 AGTTTGAGGGTAAAAATGTGATTCTTG-GA
1 AGTTTGAGGGTAAAAATGTGATTTTTGAGA
* *
16432 AGTTCGGGGGTAAAAATGTG-TTTTTG-GA
1 AGTTTGAGGGTAAAAATGTGATTTTTGAGA
* *
16460 AGTTCGAGGGTAAAAATGTAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTGATTTTTGAGA
* * * *
16490 AGTTT-AGGTGTTAAAATTTAATTTTGGAGA
1 AGTTTGAGG-GTAAAAATGTGATTTTTGAGA
* * * *
16520 AGTTTAAGGGTTAAAATGTAATTTTGGAGA
1 AGTTTGAGGGTAAAAATGTGATTTTTGAGA
* * *
16550 AGTTTAAGGGTCAAAATGGGATTTTT
1 AGTTTGAGGGTAAAAATGTGATTTTT
16576 AAAGAAAACA
Statistics
Matches: 150, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
28 25 0.17
29 34 0.23
30 88 0.59
31 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (30 bp):
AGTTTGAGGGTAAAAATGTGATTTTTGAGA
Found at i:16459 original size:28 final size:28
Alignment explanation
Indices: 16402--16493 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
16392 GATTTTTAAA
* *
16402 AAGTTTGAGGGTAAAAATGTGATTCTTGG
1 AAGTTCGAGGGTAAAAATGTG-TTTTTGG
*
16431 AAGTTCGGGGGTAAAAATGTGTTTTTGG
1 AAGTTCGAGGGTAAAAATGTGTTTTTGG
*
16459 AAGTTCGAGGGTAAAAATGTAATTTTTGAG
1 AAGTTCGAGGGTAAAAATGT-GTTTTTG-G
16489 AAGTT
1 AAGTT
16494 TAGGTGTTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
28 25 0.45
29 25 0.45
30 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (28 bp):
AAGTTCGAGGGTAAAAATGTGTTTTTGG
Found at i:19457 original size:14 final size:14
Alignment explanation
Indices: 19439--19473 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
19429 ATGCTTAGAA
19439 AAAAAAATGAAAAAG
1 AAAAAAA-GAAAAAG
19454 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
19468 AAAAAA
1 AAAAAA
19474 GAGCATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Done.