Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013925.1 Kokia drynarioides strain JFW-HI SEQ_128955, 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: 20386
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Found at i:10825 original size:156 final size:156
Alignment explanation
Indices: 10536--11023 Score: 557
Period size: 156 Copynumber: 3.2 Consensus size: 156
10526 GGCGTGGTCA
* * * *
10536 TCTTCCTGATGAGATATTAAGAAGAAGACCAAACCAAACCCACGCTCAATGTAAGCAAGTCTTCG
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCG
* * * *
10601 AATCCCAGCTTCCTGATGACACATTGAGAAGCAAATCGGAGCAATAAACGGTTAGCTTCCTGAGG
66 AATCCCAGCTTCCTGATGACACACTGAGAAGCAGATCGGAGCGATAAACGGTTAGCTTCCTGATG
10666 AGATACGGAGAAGTAGACCAAATTCG
131 AGATACGGAGAAGTAGACCAAATTCG
* *
10692 TCTTCCTGATGAGATACTGAGAAGATGACCAAACCAAACCCACGTTCGATGTGAGCAAGTCTTCG
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCG
*
10757 AATCCCAGCTTCCTGATGACACACCGAGAAGCAGATCGGAGCGATAAACGGTTAGCTTCCTGATG
66 AATCCCAGCTTCCTGATGACACACTGAGAAGCAGATCGGAGCGATAAACGGTTAGCTTCCTGATG
* * * *
10822 AGATACTGAGAAGCGT-GTCGAAGTAATTAG
131 AGATACGGAGAA--GTAGAC-CA--AATTCG
* * ** * * * *
10852 -CTTCCTAATGAGATACTGAGAAGAAAACCAAGTCAAACCCATGCTCGACGTGAGAAAATCTTCG
1 TCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCG
* * * * *
10916 AA-CCATAGCTTCCTGATGAGATACTGAGAAGC-GTATC-GA-AG-T-AA---TTAGCTTCCTAA
66 AATCC-CAGCTTCCTGATGACACACTGAGAAGCAG-ATCGGAGCGATAAACGGTTAGCTTCCTGA
*
10972 TGAGATACGGAGAAGTAGACCAAATTCA
129 TGAGATACGGAGAAGTAGACCAAATTCG
* *
11000 TCTTCCTGATGAAATACAGAGAAG
1 TCTTCCTGATGAGATACTGAGAAG
11024 CGGTTTGAAA
Statistics
Matches: 284, Mismatches: 39, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
148 4 0.01
149 20 0.07
150 3 0.01
151 2 0.01
152 24 0.08
155 2 0.01
156 131 0.46
157 3 0.01
158 8 0.03
159 82 0.29
160 5 0.02
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (156 bp):
TCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCG
AATCCCAGCTTCCTGATGACACACTGAGAAGCAGATCGGAGCGATAAACGGTTAGCTTCCTGATG
AGATACGGAGAAGTAGACCAAATTCG
Found at i:12456 original size:20 final size:20
Alignment explanation
Indices: 12437--12474 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12427 ATCAGTAATA
12437 AATAATATT-AATAAAAAAT
1 AATAATATTAAATAAAAAAT
*
12456 ATTAATATTAAATAAAAAA
1 AATAATATTAAATAAAAAA
12475 AGGAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAATATTAAATAAAAAAT
Found at i:12469 original size:13 final size:13
Alignment explanation
Indices: 12432--12462 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12422 TAGATATCAG
*
12432 TAATAAATAATAT
1 TAATAAAAAATAT
12445 TAATAAAAAATAT
1 TAATAAAAAATAT
12458 TAATA
1 TAATA
12463 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAATAAAAAATAT
Found at i:13580 original size:30 final size:30
Alignment explanation
Indices: 13546--13770 Score: 149
Period size: 30 Copynumber: 7.7 Consensus size: 30
13536 TTCCGTTTTT
13546 ACCCCCGAACTTCCAAAAATCCCATTTTCG
1 ACCCCCGAACTTCCAAAAATCCCATTTTCG
* *
13576 A-CCCCGAAACTTCTAAAAATTCCATTTT-G
1 ACCCCCG-AACTTCCAAAAATCCCATTTTCG
** *** **
13605 -CCCCTTAACTTTTGAAAATCCCATTTTTA
1 ACCCCCGAACTTCCAAAAATCCCATTTTCG
** * * * *
13634 ACCCCAAAAGTTCTAAAAATTCCA-TTTCA
1 ACCCCCGAACTTCCAAAAATCCCATTTTCG
* *
13663 ACCCCCAAACTTCCAAAAATCCCATTTTTG
1 ACCCCCGAACTTCCAAAAATCCCATTTTCG
** * * *
13693 ACCCCAAAAGTTCCAAAAATTCCA-TTTCT
1 ACCCCCGAACTTCCAAAAATCCCATTTTCG
** *
13722 A-CCGTGAACTTCCAAAAATCCCATTTT-T
1 ACCCCCGAACTTCCAAAAATCCCATTTTCG
*
13750 AACCCCGAAACTTCCAAAAAT
1 ACCCCCG-AACTTCCAAAAAT
13771 TCTGTTTCTA
Statistics
Matches: 154, Mismatches: 33, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
28 37 0.24
29 43 0.28
30 74 0.48
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.28
Consensus pattern (30 bp):
ACCCCCGAACTTCCAAAAATCCCATTTTCG
Found at i:13697 original size:59 final size:59
Alignment explanation
Indices: 13522--13873 Score: 321
Period size: 59 Copynumber: 6.0 Consensus size: 59
13512 GGAGGTCCCT
* * * * * *
13522 AAACTGTCAAAAAATTCCGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCG
1 AAACT-TCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * ** *** *
13582 AAACTTCTAAAAATTCCATTT-TGCCCCTTAACTTTTGAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
13640 AAAGTTCTAAAAATTCCATTTCAACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* *** * *
13699 AAAGTTCCAAAAATTCCATTTCTA-CCGTGAACTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
** * * * * ***
13757 AAACTTCCAAAAATTCTGTTTCTACCCCAAAATTTCAAAAAATCTCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
** * ** * * *
13816 AAACTTCCAGGAATTCCATTTTTAGACCCGAACTTCCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
13874 GAATTTTCCC
Statistics
Matches: 235, Mismatches: 55, Indels: 5
0.80 0.19 0.02
Matches are distributed among these distances:
58 98 0.42
59 132 0.56
60 5 0.02
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:13740 original size:117 final size:116
Alignment explanation
Indices: 13522--13873 Score: 391
Period size: 117 Copynumber: 3.0 Consensus size: 116
13512 GGAGGTCCCT
* * * *
13522 AAACTGTCAAAAAATTCCGTTTTTACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCGAAACT
1 AAACT-TCCAAAAATTCCGTTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * * ***
13587 TCTAAAAATTCCATTTTGCCCCTTAACTTTTGAAAATCCCATTTTTAACCCCA
65 TCCAAAAATTCCATTTTG-ACCTGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * * * *
13640 AAAGTTCTAAAAATTCCATTTCAACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAAAGTT
1 AAACTTCCAAAAATTCCGTTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
*
13705 CCAAAAATTCCATTTCT-ACCGTGAACTTCCAAAAATCCCATTTTTAACCCCG
66 CCAAAAATTCCATTT-TGACC-TGAACTTCCAAAAATCCCATTTTTAACCCCA
* * * * * **
13757 AAACTTCCAAAAATTCTGTTTCTACCCCAAAATTTCAAAAAATCTCATTTTTGACCTTGAAACTT
1 AAACTTCCAAAAATTCCGTTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
** * *
13822 CCAGGAATTCCATTTTTAGACCCGAACTTCCAAAAATTCCATTTTTAACCCC
66 CCAAAAATTCCA-TTTT-GACCTGAACTTCCAAAAATCCCATTTTTAACCCC
13874 GAATTTTCCC
Statistics
Matches: 196, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
116 2 0.01
117 155 0.79
118 36 0.18
119 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (116 bp):
AAACTTCCAAAAATTCCGTTTCTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTT
CCAAAAATTCCATTTTGACCTGAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:13838 original size:30 final size:29
Alignment explanation
Indices: 13817--13872 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
13807 TTGACCTTGA
**
13817 AACTTCCAGGAATTCCATTTTTAGACCCG
1 AACTTCCAAAAATTCCATTTTTAGACCCG
13846 AACTTCCAAAAATTCCATTTTTA-ACCC
1 AACTTCCAAAAATTCCATTTTTAGACCC
13873 CGAATTTTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTAGACCCG
Found at i:13939 original size:28 final size:29
Alignment explanation
Indices: 13885--13944 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
13875 AATTTTCCCT
13885 AAATTACCATTTCACCCTCGAGAATCC-A
1 AAATTACCATTTCACCCTCGAGAATCCGA
** * *
13913 AAATTACCATTTTGCCCTCGGGTATCCGA
1 AAATTACCATTTCACCCTCGAGAATCCGA
13942 AAA
1 AAA
13945 GTCTCATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (29 bp):
AAATTACCATTTCACCCTCGAGAATCCGA
Found at i:15019 original size:21 final size:21
Alignment explanation
Indices: 14994--15034 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
14984 CTATTTTAAG
**
14994 TTTTAAGTAAATGTTTTAGTC
1 TTTTAAGTAAAAATTTTAGTC
15015 TTTTAAGTAAAAATTTTAGT
1 TTTTAAGTAAAAATTTTAGT
15035 AATCCATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTTAAGTAAAAATTTTAGTC
Found at i:15112 original size:3 final size:3
Alignment explanation
Indices: 15104--15130 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
15094 TGAGAACTCA
15104 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
15131 GTAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19707 original size:20 final size:20
Alignment explanation
Indices: 19682--19720 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19672 GATGAAAGTT
19682 GTATTTCACAACGTTCTAAA
1 GTATTTCACAACGTTCTAAA
* *
19702 GTATTTCATAGCGTTCTAA
1 GTATTTCACAACGTTCTAA
19721 CCGAATGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATTTCACAACGTTCTAAA
Done.