Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000963.1 Kokia drynarioides strain JFW-HI SEQ_112141, 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: 14785
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Found at i:565 original size:20 final size:20
Alignment explanation
Indices: 540--581 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
530 GATCCTAAAA
*
540 TTGAATTTAATTATT-TTCTT
1 TTGAATTAAATT-TTATTCTT
560 TTGAATTAAATTTTATTCTT
1 TTGAATTAAATTTTATTCTT
580 TT
1 TT
582 CAATATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TTGAATTAAATTTTATTCTT
Found at i:1219 original size:24 final size:24
Alignment explanation
Indices: 1181--1226 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1171 TCAATAAACA
* *
1181 TCTTTGGTATGCTACTCTAGCATG
1 TCTTTGGTATACTACTCCAGCATG
*
1205 TCTTTGGTCTACTACTCCAGCA
1 TCTTTGGTATACTACTCCAGCA
1227 CCTTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.39
Consensus pattern (24 bp):
TCTTTGGTATACTACTCCAGCATG
Found at i:8490 original size:41 final size:41
Alignment explanation
Indices: 8430--8565 Score: 107
Period size: 41 Copynumber: 3.3 Consensus size: 41
8420 ATTCGTAAAA
* * * *
8430 CTTCCTCTTTAGACGATCTTAAT-CTTCACAAAATCGTAAGT
1 CTTCCTTTTTAAACAATCTTAATCCTT-ACAAAATCATAAGT
** * *
8471 CTTCCTTTTTAAACAATCTT-ATGCCTTACCGAGTCATCAGT
1 CTTCCTTTTTAAACAATCTTAAT-CCTTACAAAATCATAAGT
* ** * *
8512 CTTCCTTTTTAAACAATCTT-ATGCTCTACCGAGTTATAAGT
1 CTTCCTTTTTAAACAATCTTAATCCT-TACAAAATCATAAGT
8553 CTTCCTTTTTAAA
1 CTTCCTTTTTAAA
8566 TGTAATCTCA
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.91
42 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.40
Consensus pattern (41 bp):
CTTCCTTTTTAAACAATCTTAATCCTTACAAAATCATAAGT
Found at i:8615 original size:43 final size:44
Alignment explanation
Indices: 8468--8729 Score: 206
Period size: 43 Copynumber: 6.2 Consensus size: 44
8458 CAAAATCGTA
* * * *
8468 AGTCTTCCTTTTTAAAC--AATCTTATGC-CTTACCGAGTCATC
1 AGTCTTCCTTTTTAAACATAATCTCATGCTCATACCGAGACATG
* ** *
8509 AGTCTTCCTTTTTAAAC--AATCTTATGCTC-TACCGAGTTATA
1 AGTCTTCCTTTTTAAACATAATCTCATGCTCATACCGAGACATG
** *
8550 AGTCTTCCTTTTTAAATGTAATCTCATGCTCATTCCGAGACATG
1 AGTCTTCCTTTTTAAACATAATCTCATGCTCATACCGAGACATG
* * * *
8594 AGTCTTCC-TTTAAAACATAATCTCATTCTCATCCCGAGACTTG
1 AGTCTTCCTTTTTAAACATAATCTCATGCTCATACCGAGACATG
* * * * *
8637 AGTCTTCC--TTTAAACATATTTTCATGCTCATTCCGAGTCACG
1 AGTCTTCCTTTTTAAACATAATCTCATGCTCATACCGAGACATG
* * *
8679 AGT-TTTCTATTTATACA-AATTCTCATGCTCA-ACTCGAGACATG
1 AGTCTTCCTTTTTAAACATAA-TCTCATGCTCATAC-CGAGACATG
*
8722 AGTTTTCC
1 AGTCTTCC
8730 ATTTATACAT
Statistics
Matches: 182, Mismatches: 30, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
41 56 0.31
42 32 0.18
43 75 0.41
44 19 0.10
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (44 bp):
AGTCTTCCTTTTTAAACATAATCTCATGCTCATACCGAGACATG
Found at i:8703 original size:85 final size:86
Alignment explanation
Indices: 8573--8739 Score: 196
Period size: 85 Copynumber: 2.0 Consensus size: 86
8563 AAATGTAATC
* * * *
8573 TCATGCTCATTCCGAGACATGAGTCTTCCTTTAAAACATAATCTCATTCTCATCCCGAGACTTGA
1 TCATGCTCATTCCGAGACACGAGTCTTCCTTTAAAACATAATCTCATGCTCAACCCGAGACATGA
8638 GTCTTCC-TTTAAACATATTT
66 GTCTTCCATTTAAACATATTT
* * * * *
8658 TCATGCTCATTCCGAGTCACGAGT-TTTCTATTTATACA-AATTCTCATGCTCAACTCGAGACAT
1 TCATGCTCATTCCGAGACACGAGTCTTCCT-TTAAAACATAA-TCTCATGCTCAACCCGAGACAT
* *
8721 GAGTTTTCCATTTATACAT
64 GAGTCTTCCATTTAAACAT
8740 CAAGTGTTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
84 6 0.09
85 54 0.79
86 8 0.12
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (86 bp):
TCATGCTCATTCCGAGACACGAGTCTTCCTTTAAAACATAATCTCATGCTCAACCCGAGACATGA
GTCTTCCATTTAAACATATTT
Found at i:12489 original size:27 final size:27
Alignment explanation
Indices: 12450--12502 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
12440 AAAATTCAAG
*
12450 GTAAAATTTGAGTACTAAAGTGTAAAA
1 GTAAAATTAGAGTACTAAAGTGTAAAA
12477 GTAAAATTAGAGTACTAAAGTGTAAA
1 GTAAAATTAGAGTACTAAAGTGTAAA
12503 TAACACTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (27 bp):
GTAAAATTAGAGTACTAAAGTGTAAAA
Found at i:13483 original size:41 final size:41
Alignment explanation
Indices: 13428--13693 Score: 203
Period size: 41 Copynumber: 6.3 Consensus size: 41
13418 GTTTATGTCA
* * *
13428 AAGCACCGCCAAAGGTCAGGTCATTAGCGGCGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCCCAT
** **
13469 AAGCGCCGCTAAAGGTCAGGTTATTAGCGGATCATGGCTTTATCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGG--C---GCTTTCCCAT
* * *
13515 AAGCACCGCTAAAGGTCAGGGCATTTGCGACGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCCCAT
* * ** ** * * **
13556 AAGCGCCACTAGAGGTCAGGGCCGCTAAAGGTTAAGGCATT-AGA-
1 AAGCGCCGCTAAAGGTCAGGG-CATTAGCGG----CGCTTTCCCAT
* *
13600 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCACTTTCTCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCCCAT
* * *
13641 AAGCACCGCTAAAGGCCAGGGCATTAACGGCGCTTTCCCAT
1 AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCCCAT
13682 AAGCGCCGCTAA
1 AAGCGCCGCTAA
13694 TTTATTTAAA
Statistics
Matches: 171, Mismatches: 42, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
39 3 0.02
40 1 0.01
41 100 0.58
42 3 0.02
43 6 0.04
44 20 0.12
45 1 0.01
46 37 0.22
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGGGCATTAGCGGCGCTTTCCCAT
Found at i:14479 original size:170 final size:170
Alignment explanation
Indices: 14194--14693 Score: 797
Period size: 170 Copynumber: 3.0 Consensus size: 170
14184 GTTGGAACAG
* *
14194 TAACAATGAAAATGGCACCCTCTTTAGTGAGA-T-TATATGAACAAATGCCCAAACCTAAATATG
1 TAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATG
* * * *
14257 TTATTGCTATGAGCACGTGTACAATTACAGGAGGGATGTTCAATAATGATTCTTATAGTATTGTT
66 TTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATATTGATTCTTATAGTACTGTT
*
14322 CGAGGGGTCGATAAGCTAATTCCCGTGGATGTCTATACAA
131 CGAGGGGTCGATAAGCTAATTCCCATGGATGTCTATACAA
* ***
14362 TAATAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGTTTGAACCTAAATATG
1 TAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATG
* *
14427 TTATTGTTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATATTGATTCTTATAGTACTATT
66 TTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATATTGATTCTTATAGTACTGTT
* * * *
14492 TGGGGGGTCGATAAGCTAATTCCCATGGATGTCTATATAG
131 CGAGGGGTCGATAAGCTAATTCCCATGGATGTCTATACAA
*
14532 TAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGGCCGAACCTAAATATG
1 TAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATG
* *
14597 TTATTGCTATGGGAGCGTGTACAATTACAGGAGGGATGTTCAGTATTGATTCTTATAGTACTGTT
66 TTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATATTGATTCTTATAGTACTGTT
*
14662 CGAGGGGTGGATAAGCTAATTCCCATGGATGT
131 CGAGGGGTCGATAAGCTAATTCCCATGGATGT
14694 GTATTTGTCG
Statistics
Matches: 302, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
168 30 0.10
169 1 0.00
170 271 0.90
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (170 bp):
TAACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATG
TTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATATTGATTCTTATAGTACTGTT
CGAGGGGTCGATAAGCTAATTCCCATGGATGTCTATACAA
Found at i:14772 original size:17 final size:17
Alignment explanation
Indices: 14745--14784 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
14735 ATAAATTCTA
*
14745 AATAGACTAAATATAAAT
1 AATA-ACTAAATAAAAAT
14763 AATAACTAAATAAAAAT
1 AATAACTAAATAAAAAT
14780 AATAA
1 AATAA
14785 T
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (17 bp):
AATAACTAAATAAAAAT
Done.