Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010363.1 Kokia drynarioides strain JFW-HI SEQ_125234, 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: 34995
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:1582 original size:13 final size:13
Alignment explanation
Indices: 1539--1603 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
1529 TTAAACCAAG
*
1539 TTTTTCAAGAGTAA
1 TTTTTCAAAAGT-A
1553 TTTTT-AAAA-TCA
1 TTTTTCAAAAGT-A
* *
1565 CTTTTCCAAAGTA
1 TTTTTCAAAAGTA
*
1578 TTTTTTAAAAGTA
1 TTTTTCAAAAGTA
*
1591 TTTCTCAAAAGTA
1 TTTTTCAAAAGTA
1604 ATGTTAAACT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
12 6 0.15
13 28 0.70
14 6 0.15
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTTCAAAAGTA
Found at i:3616 original size:2 final size:2
Alignment explanation
Indices: 3609--3645 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3599 GTAATACGTT
3609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3646 TATTAGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4673 original size:19 final size:18
Alignment explanation
Indices: 4638--4693 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
4628 AAACTAATTA
*
4638 ATAATAATAAATAAAATATT
1 ATAATAA-AATTAAAATA-T
4658 ATAATAAAATTAAAATAT
1 ATAATAAAATTAAAATAT
4676 ATAA-AAAGCATTAAAATA
1 ATAATAAA--ATTAAAATA
4694 AAAATTTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 3 0.09
18 5 0.15
19 18 0.55
20 7 0.21
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAATAAAATTAAAATAT
Found at i:8993 original size:24 final size:24
Alignment explanation
Indices: 8965--9019 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
8955 TAGACTAATA
* *
8965 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
* * *
8989 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
9013 AGAGTTT
1 AGAGTTT
9020 TAACAGAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:9028 original size:25 final size:24
Alignment explanation
Indices: 8977--9028 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
8967 AGTTTGACTC
* **
8977 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACAG
*
9001 AAACAATTAAACAGAGTTTTAACAG
1 AAACAAATAAACAGAG-TTTAACAG
9026 AAA
1 AAA
9029 GATTATTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACAG
Found at i:9618 original size:19 final size:20
Alignment explanation
Indices: 9594--9642 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
9584 AAATGCATAA
*
9594 ATATTTTTTATTTT-TT-TAT
1 ATATTTTTAATTTTATTCT-T
9613 ATATTTTTAATTTTATTCTT
1 ATATTTTTAATTTTATTCTT
9633 ATATTTTTAA
1 ATATTTTTAA
9643 AAATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.48
20 13 0.48
21 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
ATATTTTTAATTTTATTCTT
Found at i:9651 original size:24 final size:25
Alignment explanation
Indices: 9624--9682 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
9614 TATTTTTAAT
*
9624 TTTATTCTTATA-TTTTTAAAAATA
1 TTTATTATTATATTTTTTAAAAATA
*
9648 TTTATTATTATATTTTTTGAAAATA
1 TTTATTATTATATTTTTTAAAAATA
9673 TTTATATATT
1 TTTAT-TATT
9683 TTTATACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 11 0.35
25 16 0.52
26 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATTATTATATTTTTTAAAAATA
Found at i:10628 original size:97 final size:96
Alignment explanation
Indices: 10450--10635 Score: 234
Period size: 97 Copynumber: 1.9 Consensus size: 96
10440 GAAAAGGACG
** *
10450 TTCGATTATCTCAATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAATTAAGGCGCAAATTTTCAGAATCGA
*
10515 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
* * * *
10546 TTCGATTATTTCGATTTGAAGAAAAAATTGTACCTAGTAAATTAAGGCGTAAATTTTC-GAAACT
1 TTCGATTATCTCAATTTGAAG-AAAAATTGCACCTAGTAAATTAAGGCGCAAATTTTCAG-AA-T
*
10610 CGAA-ATAAA-AGAATATTGCCTCGATT
63 CGAAGATAAAGA-AACATTGCCTCGATT
10636 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
96 21 0.27
97 51 0.66
98 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAATTAAGGCGCAAATTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:10994 original size:58 final size:60
Alignment explanation
Indices: 10840--11329 Score: 371
Period size: 58 Copynumber: 8.3 Consensus size: 60
10830 ATCGGAGTTG
* * * * * * **
10840 AAAATGAGACTTTTTGGATACTT-GAGGGCAAAATGGTAA-TTTTGGGAAGATTCGGGGTTT
1 AAAATG-GAATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
* * * * * *
10900 AAAATGGAATTATT-AAACATTCGA-GGTAAAAGGGTAA-TTTTGAG-AGTTTCAAGGTCG
1 AAAATGGAATTTTTGGAA-GTTCGAGGGTAAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
*
10957 AAAATGGAGTTTTTGGACA-TTCGAGGGTAAAATGGTAA-TTTTGA-AAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
* * *
11015 AAATTGGATTTTTTGGAAGTTCGAGGGTAAAAATGG-AATTTTTG-GAAGTTT-TAGGATCAA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGAGAAGTTTCGAGG-TC-A
*
11075 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGG-AATTTTTGA-AAGTTT-GAGGGT-A
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGAGAAGTTTCGA-GGTCA
* * *
11133 AAAATGGAA-TTTTGGAAGTTCAAGGGTAAAATTGTAATTTTTG-GAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
* * * * ** * *
11191 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAAT-ATAA-TTTTCAAAAGTTTTAAGAT-T
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
* * * * * *
11249 AAAATGGAATTTTTGGAAGTTCGGGGGTAAAAAAT-ATAATTTTTTA-AAGTTTTGGGGT-T
1 AAAATGGAATTTTTGGAAGTTCGAGGGT--AAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
11308 AAAATGGAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGA-AGTT
11330 TAGGGGCCTT
Statistics
Matches: 361, Mismatches: 45, Indels: 48
0.80 0.10 0.11
Matches are distributed among these distances:
56 6 0.02
57 60 0.17
58 130 0.36
59 93 0.26
60 70 0.19
61 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAGAAGTTTCGAGGTCA
Found at i:11035 original size:30 final size:29
Alignment explanation
Indices: 10869--11330 Score: 272
Period size: 29 Copynumber: 15.8 Consensus size: 29
10859 ACTTGAGGGC
* * * *
10869 AAAATGGTAATTTTGGGAAGATTCGGGGTTT
1 AAAATGG-AATTTTTGGAAGTTTCGAGG-TA
* * **
10900 AAAATGGAATTATT-AAACATTCGAGGT-
1 AAAATGGAATTTTTGGAAGTTTCGAGGTA
* * *
10927 AAAAGGGTAA-TTTT-GAGAGTTTCAAGGTCG
1 AAAATGG-AATTTTTGGA-AGTTTCGAGGT-A
*
10957 AAAATGGAGTTTTTGGACA--TTCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTCGA-GGTA
*
10985 AAAATGGTAA-TTTTGAAAGTTTCGAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGAGGT-A
* *
11015 AAATTGGATTTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTA
*
11044 AAAATGGAATTTTTGGAAGTTT-TAGGATCAA
1 AAAATGGAATTTTTGGAAGTTTCGAGG-T--A
*
11075 AAAATGGAATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GAGGTA
*
11104 AAAATGGAATTTTTGAAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTA
*
11133 AAAATGGAA-TTTTGGAAG-TTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTA
* * *
11161 AAATTGTAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGAGGT-A
11191 AAAATGGAATTTTTGGAAGTTT-GAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGA-GGTA
** *** ** * *
11220 AAAATATAATTTTCAAAAGTTTTAAGATT
1 AAAATGGAATTTTTGGAAGTTTCGAGGTA
*
11249 AAAATGGAATTTTTGGAAG-TTCGGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTC-GAGGT-A
** ** * * *
11279 AAAATATAATTTTTTAAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTCGAGGTA
11308 AAAATGGAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
11331 AGGGGCCTTT
Statistics
Matches: 335, Mismatches: 64, Indels: 65
0.72 0.14 0.14
Matches are distributed among these distances:
27 13 0.04
28 53 0.16
29 140 0.42
30 94 0.28
31 33 0.10
32 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGAGGTA
Found at i:11319 original size:88 final size:86
Alignment explanation
Indices: 10984--11330 Score: 344
Period size: 89 Copynumber: 3.9 Consensus size: 86
10974 CATTCGAGGG
* * * * * *
10984 TAAAATGGTAA-TTTTGAAAGTTTC-GAGGTCAAAATTGGATTTTTTGGAAGTTCGAGGGTAAAA
1 TAAAATGG-AATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGAAAGTTTGAGGGTAAAA
*
11047 ATGGAATTTTTGGAAGTTTTAGGAT
63 ATGGAA-TTTTGGAAGTTTTAAGAT
*
11072 CAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGTTTGAGGGTAAAAA
1 --TAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGTTTGAGGGTAAAAA
* **
11137 TGGAATTTTGGAAG-TTCAAGGG
64 TGGAATTTTGGAAGTTTTAAGAT
* *
11159 TAAAATTGTAATTTTTGGAAGTTTC-GGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAA
1 TAAAA-TGGAATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGAAAGTTTGAGGGTAAAA
** **
11223 ATATAATTTTCAAAAGTTTTAAGAT
63 ATGGAATTTT-GGAAGTTTTAAGAT
** * *
11248 TAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAAATATAATTTTTTAAAGTTTTG-GGGTTAAAA
1 TAAAATGGAATTTTTGGAAGTTCGGGGGT-AAAAATGGAATTTTTGAAAG-TTTGAGGGTAAAAA
11312 TGGAATTTTTGGATAGTTT
64 TGGAA-TTTTGGA-AGTTT
11331 AGGGGCCTTT
Statistics
Matches: 214, Mismatches: 32, Indels: 23
0.80 0.12 0.09
Matches are distributed among these distances:
85 4 0.02
86 19 0.09
87 50 0.23
88 59 0.28
89 63 0.29
90 19 0.09
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (86 bp):
TAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGTTTGAGGGTAAAAATG
GAATTTTGGAAGTTTTAAGAT
Found at i:13021 original size:17 final size:17
Alignment explanation
Indices: 12983--13047 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
12973 CAAATTTGAT
12983 TAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTT---AAGA
*
13003 TAATTTTAAATTTAAGA
1 TAAATTTAAATTTAAGA
*
13020 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTT-AAGA
13038 TAAATTTAAA
1 TAAATTTAAA
13048 CCTAATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
17 16 0.39
18 13 0.32
20 12 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:34508 original size:31 final size:31
Alignment explanation
Indices: 34473--34531 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
34463 ATTTTAATTT
* *
34473 TTGAGAGGCCTAATTAAAATTTTGAAAAATG
1 TTGAGAGGACTAATGAAAATTTTGAAAAATG
* *
34504 TTGAGAGGATTAGTGAAAATTTTGAAAA
1 TTGAGAGGACTAATGAAAATTTTGAAAA
34532 CTCCAAGGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.32
Consensus pattern (31 bp):
TTGAGAGGACTAATGAAAATTTTGAAAAATG
Found at i:34727 original size:30 final size:29
Alignment explanation
Indices: 34663--34729 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
34653 GTAGAGCTTG
* * * *
34663 AAAATTTTAAAAATTTAAGGGTTTATTTA
1 AAAAATTTAAAAATTAAAGGGCTTATATA
34692 AAAAATTTAAAAAGTTAAAGGGCTTA-ATA
1 AAAAATTTAAAAA-TTAAAGGGCTTATATA
34721 ATAAAATTT
1 A-AAAATTT
34730 TCAAATACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.37
Consensus pattern (29 bp):
AAAAATTTAAAAATTAAAGGGCTTATATA
Done.