Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006296.1 Kokia drynarioides strain JFW-HI SEQ_120869, 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: 50514
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7932 original size:29 final size:30
Alignment explanation
Indices: 7870--8356 Score: 347
Period size: 29 Copynumber: 16.5 Consensus size: 30
7860 CTTCAAGAAC
7870 AAAATGGTAATTTTT-GAAAGGTTC-AGGGTTA
1 AAAATGG-AATTTTTGGAAA-GTTCGAGGG-TA
* * *
7901 AAAATGGAATTTTTAGATA-TTTGAGGGT-
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
* * *
7929 AAAATGGTAATATTTGGAACGTTCG-GGATTA
1 AAAATGG-AATTTTTGGAAAGTTCGAGG-GTA
* * * *
7960 AACATGGAATTTTTAGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
*
7988 AAAATGGTAATTTTT-GAAAGTTTG-GGGTCAAA
1 AAAATGG-AATTTTTGGAAAGTTCGAGGGT---A
8020 AAAATGGAA-TTTTGGAAAGTTCG-GTGGTA
1 AAAATGGAATTTTTGGAAAGTTCGAG-GGTA
* ** *
8049 AAAAT-GTATTTTTCAAAAAGTTCGA-GGTC
1 AAAATGGAATTTTT-GGAAAGTTCGAGGGTA
*
8078 AAAATGGAA-TTTTGGAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
* *
8107 AAAATGTAATTTTTAGAAAGTTC-AGGGTCA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGT-A
* *
8137 AAAAT-GAAATTTTGGAAAGTTCGAGTGTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
* *
8166 AAAATGTAATTTTTGGAAAGTTCG-GTGTCA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGT-A
* *
8196 AAAATGGAA--TTTGGAATGTTCGAGGGTG
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
* *
8224 AAAATGTAATTTATGGAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
* *
8254 AAAATGTAATTTTTAGATAA-TTC-AGGGTTA
1 AAAATGGAATTTTTGGA-AAGTTCGAGGG-TA
* * * *
8284 AAAAT-AAAATTTTCGAAAGTT-TAGGGTTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGG-TA
*
8313 AAAATGGAA-TTTTGGAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAAGTTCGAGGGTA
**
8342 AAAATATAATTTTTG
1 AAAATGGAATTTTTG
8357 AATAGTTTAG
Statistics
Matches: 367, Mismatches: 54, Indels: 71
0.75 0.11 0.14
Matches are distributed among these distances:
28 52 0.14
29 139 0.38
30 137 0.37
31 29 0.08
32 10 0.03
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAGTTCGAGGGTA
Found at i:8097 original size:58 final size:60
Alignment explanation
Indices: 7870--8363 Score: 411
Period size: 59 Copynumber: 8.4 Consensus size: 60
7860 CTTCAAGAAC
* * * *
7870 AAAATGGTAATTTTT-GAAAGGTTC-AGGGTTAAAAATGGAATTTTTAGATA-TTTGAGGGT-
1 AAAAT-GTAATTTTTAGAAA-GTTCGAGGGTCAAAAATGGAA-TTTTGGAAAGTTCGAGGGTA
* * * * * * * * *
7929 AAAATGGTAATATTTGGAACGTTCG-GGATTAAACATGGAATTTTTAGACA-TTCGGGGGT-
1 AAAAT-GTAATTTTTAGAAAGTTCGAGGGTCAAAAATGGAA-TTTTGGAAAGTTCGAGGGTA
*
7988 AAAATGGTAATTTTT-GAAAGTTTG-GGGTCAAAAAAATGGAATTTTGGAAAGTTCG-GTGGTA
1 AAAAT-GTAATTTTTAGAAAGTTCGAGGGTC--AAAAATGGAATTTTGGAAAGTTCGAG-GGTA
* *
8049 AAAATGT-ATTTTTCAAAAAGTTCGA-GGTC-AAAATGGAATTTTGGAAAGTTTGAGGGTA
1 AAAATGTAATTTTT-AGAAAGTTCGAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
* *
8107 AAAATGTAATTTTTAGAAAGTTC-AGGGTCAAAAATGAAATTTTGGAAAGTTCGAGTGTA
1 AAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
* * * *
8166 AAAATGTAATTTTTGGAAAGTTCG-GTGTCAAAAATGGAA-TTTGGAATGTTCGAGGGTG
1 AAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
* * * *
8224 AAAATGTAATTTATGGAAAGTTCGAGGGT-AAAAATGTAATTTTTAGATAA-TTC-AGGGTTA
1 AAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAATGGAA-TTTTGGA-AAGTTCGAGGG-TA
* * * * * *
8284 AAAAT-AAAATTTTCGAAAGTT-TAGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTA
1 AAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
*
8342 AAAATATAATTTTT-GAATAGTT
1 AAAATGTAATTTTTAGAA-AGTT
8364 TAGGGACCTT
Statistics
Matches: 366, Mismatches: 44, Indels: 50
0.80 0.10 0.11
Matches are distributed among these distances:
57 3 0.01
58 126 0.34
59 185 0.51
60 35 0.10
61 17 0.05
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (60 bp):
AAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
Found at i:8243 original size:88 final size:88
Alignment explanation
Indices: 7870--8356 Score: 367
Period size: 88 Copynumber: 5.5 Consensus size: 88
7860 CTTCAAGAAC
* * * * *
7870 AAAATGGTAATTTTTGAAAGGTTC-AGGGTTAAAAATGGAATTTTTAGATA-TTTGAGGGT--AA
1 AAAAT-GTAATTTTGGAAA-GTTCGAGGG-TAAAAATGTAATTTTTGGAAAGTTCG-GGGTCAAA
* *
7931 AATGGTAATATTTGGAACGTTCG-GGATTA
62 AATGG-AAT-TTTGGAAAGTTCGAGG-GTA
* * * * * *
7960 AACATGGAATTTTTAGACA-TTCGGGGGT-AAAATGGTAATTTTT-GAAAGTTTGGGGTCAAAAA
1 AAAATGTAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAGTTCGGGGTC--AAA
8022 AATGGAATTTTGGAAAGTTCG-GTGGTA
62 AATGGAATTTTGGAAAGTTCGAG-GGTA
* ** * * *
8049 AAAATGTATTTTTCAAAAAGTTCGA-GGTCAAAATGGAA-TTTTGGAAAGTTTGAGGGT-AAAAA
1 AAAATGTAATTTT-GGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTCG-GGGTCAAAAA
* *
8111 TGTAATTTTTAGAAAGTTC-AGGGTCA
64 TGGAA-TTTTGGAAAGTTCGAGGGT-A
* * *
8137 AAAATGAAATTTTGGAAAGTTCGAGTGTAAAAATGTAATTTTTGGAAAGTTCGGTGTCAAAAATG
1 AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATG
* *
8202 GAA-TTTGGAATGTTCGAGGGTG
66 GAATTTTGGAAAGTTCGAGGGTA
* * *
8224 AAAATGTAATTTATGGAAAGTTCGAGGGTAAAAATGTAATTTTTAGATAA-TTCAGGGTTAAAAA
1 AAAATGTAATTT-TGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGA-AAGTTCGGGGTCAAAAA
** * *
8288 TAAAATTTTCGAAAGTT-TAGGGTTA
64 TGGAATTTTGGAAAGTTCGAGGG-TA
* * *
8313 AAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTG
1 AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTG
8357 AATAGTTTAG
Statistics
Matches: 325, Mismatches: 47, Indels: 52
0.77 0.11 0.12
Matches are distributed among these distances:
87 54 0.17
88 146 0.45
89 90 0.28
90 28 0.09
91 7 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (88 bp):
AAAATGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTCGGGGTCAAAAATG
GAATTTTGGAAAGTTCGAGGGTA
Found at i:10171 original size:17 final size:17
Alignment explanation
Indices: 10152--10209 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
10142 GGAATAATTT
* *
10152 TAAATTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
10169 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
*
10187 CAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
10204 TAAATT
1 TAAATT
10210 CAAAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:10177 original size:11 final size:12
Alignment explanation
Indices: 10150--10224 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 12
10140 TTGGAATAAT
10150 TTTAAATTTAAA
1 TTTAAATTTAAA
*
10162 CTTAAA-TTAAA
1 TTTAAATTTAAA
10173 TTTAAATTTTAAA
1 TTTAAA-TTTAAA
**
10186 -ACAAATTTAAA
1 TTTAAATTTAAA
*
10197 TTTAAA-ATAAA
1 TTTAAATTTAAA
* *
10208 TTCAAA-ATAAA
1 TTTAAATTTAAA
10219 TTTAAA
1 TTTAAA
10225 ATGGGTTTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
11 35 0.69
12 11 0.22
13 5 0.10
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:10204 original size:7 final size:6
Alignment explanation
Indices: 10150--10224 Score: 59
Period size: 6 Copynumber: 13.0 Consensus size: 6
10140 TTGGAATAAT
* **
10150 TTTAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTTAAA -ACAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA
* * *
10197 TTTAAA -ATAAA TTCAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
10225 ATGGGTTTAG
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
5 15 0.28
6 32 0.60
7 6 0.11
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:27637 original size:3 final size:3
Alignment explanation
Indices: 27610--27676 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
27600 GAGGGTATTA
*
27610 AAG AAA AAG AA- AAG -AG AAG AA- AAG AAG AAGG AA- AAG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG
27651 AAG AAAG AAG AAG AAG AAG AAG AAG A
1 AAG -AAG AAG AAG AAG AAG AAG AAG A
27677 TGTTGCCCCA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
2 10 0.18
3 39 0.71
4 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27657 original size:24 final size:25
Alignment explanation
Indices: 27610--27673 Score: 89
Period size: 24 Copynumber: 2.6 Consensus size: 25
27600 GAGGGTATTA
*
27610 AAGAAAAAGAA-AAGAGAAGAAAAG
1 AAGAAGAAGAAGAAGAGAAGAAAAG
27634 AAGAAGGAA-AAGAAGAGAAG-AAAG
1 AAGAA-GAAGAAGAAGAGAAGAAAAG
27658 AAGAAGAAGAAGAAGA
1 AAGAAGAAGAAGAAGA
27674 AGATGTTGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 3 0.08
24 23 0.64
25 10 0.28
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (25 bp):
AAGAAGAAGAAGAAGAGAAGAAAAG
Found at i:41805 original size:2 final size:2
Alignment explanation
Indices: 41800--41838 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41790 AAAAAAAAAA
41800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41839 ATAAATGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48735 original size:193 final size:195
Alignment explanation
Indices: 48462--48829 Score: 485
Period size: 195 Copynumber: 1.9 Consensus size: 195
48452 CTGTACTATA
** * *
48462 AACTATTCCCTAACGATGCTGCTCACACGAGAGCTGTCGAGAGTATGCATAAAGCATAGTCCCAG
1 AACTATTCCCTAACGATGCTGCTCACACGAGAGCAATCGAGACTATGCATAAAGCATAATCCCAG
* *
48527 CCATAGTAGGGCTTGTAATCCATT-TAGGATCCATATATC-TTT-CTCAAGTCACGATGCTGCTC
66 CCATAGTAAGGCTTGTAATCCATTCTAGGATCCATATATCATTTCCT-AACTCACGATGCTGCTC
* * *
48589 GCACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTTAACCATCAATACAATATATGTGCATA
130 ACACGAGCTATCAAGGACTCGCAACATATGCGGTACCTTAACCATCAATACAATATATGTGCATA
48654 T
195 T
* * * * * *
48655 AACTATTGCCTAATGATGTTGCTCACAC-A-AGCAATCGAGACTATGCACTTATGCATAAATCTC
1 AACTATTCCCTAACGATGCTGCTCACACGAGAGCAATCGAGACTATGCA-TAAAGCAT-AATCCC
* * * * * *
48718 AGCCATCGTAAGGCTTGTAATCCATTCTTGGATTCTTTTATCATTTCCTTACTCACGATGCTGCT
64 AGCCATAGTAAGGCTTGTAATCCATTCTAGGATCCATATATCATTTCCTAACTCACGATGCTGCT
48783 CACACGAGCTATCAAGGACTCGCAACATATGCGGTACCTTAACCATC
129 CACACGAGCTATCAAGGACTCGCAACATATGCGGTACCTTAACCATC
48830 GCGTTGATTT
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
191 15 0.10
192 7 0.05
193 53 0.36
194 11 0.07
195 61 0.41
196 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (195 bp):
AACTATTCCCTAACGATGCTGCTCACACGAGAGCAATCGAGACTATGCATAAAGCATAATCCCAG
CCATAGTAAGGCTTGTAATCCATTCTAGGATCCATATATCATTTCCTAACTCACGATGCTGCTCA
CACGAGCTATCAAGGACTCGCAACATATGCGGTACCTTAACCATCAATACAATATATGTGCATAT
Done.