Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003026.1 Kokia drynarioides strain JFW-HI SEQ_115547, 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: 31838
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:6076 original size:106 final size:106
Alignment explanation
Indices: 5891--6100 Score: 280
Period size: 106 Copynumber: 2.0 Consensus size: 106
5881 TGCCTAGCAG
* *
5891 ATAACAATAAATGAGCCCAGCTCTAGTTGGATTAACCAACGATTTTACATCCAACGCTAGTCGAA
1 ATAACAATAAATGAGCCCAGCTCTAGTTGGAGTAACCAACGATTTTACACCCAACGCTAGTCGAA
* * *
5956 TAAACTGACAAATGTGTGCCTAGCACTAGTAAGTTAAACTA
66 TAAACTGACAAATGTATGCCCAGCACCAGTAAGTTAAACTA
* * * * *
5997 ATAACAATAAGTGAGCCCTGCT-TCAGTTGGAGTAACCAAC-AGTTTTGCACCCAGCGTTAGTCG
1 ATAACAATAAATGAGCCCAGCTCT-AGTTGGAGTAACCAACGA-TTTTACACCCAACGCTAGTCG
* *
6060 AATAAACTGACAAATGTATGCCCAGGACCAGTTAGTTAAAC
64 AATAAACTGACAAATGTATGCCCAGCACCAGTAAGTTAAAC
6101 AGACGAAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 2 0.02
106 88 0.98
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (106 bp):
ATAACAATAAATGAGCCCAGCTCTAGTTGGAGTAACCAACGATTTTACACCCAACGCTAGTCGAA
TAAACTGACAAATGTATGCCCAGCACCAGTAAGTTAAACTA
Found at i:9401 original size:132 final size:132
Alignment explanation
Indices: 9232--9495 Score: 393
Period size: 132 Copynumber: 2.0 Consensus size: 132
9222 TACACGATGC
* * * * *
9232 TGCTCACACGAGTTATGGGTCGAGATGTTAGGCTACACGATGCTGCTCCCATGAGCTGTGGAGAA
1 TGCTCACACGAGCTATGGGTCAAGATGTTAAGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
* * * * * * *
9297 TCCGCAATCAATGTAAGACCTCAGCCATCGGTAGGACATCTAAGACTAGCACCTATATACCTTGT
66 TCCGCAACCAATGCAAGACCTCAACCATCGGTAGAACATCTAAGACCAGCACCCATATAACTTGT
9362 AA
131 AA
* *
9364 TGCTCACACGAGCTGTGGGTCAAGATGTTAATCTACACGATGCTGCTCACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTATGGGTCAAGATGTTAAGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
*
9429 TCCGCAACCAATGCAGGACCTCAACCATCGGTAGAACATCTAAGACCAGCACCCATATAACTTGT
66 TCCGCAACCAATGCAAGACCTCAACCATCGGTAGAACATCTAAGACCAGCACCCATATAACTTGT
9494 AA
131 AA
9496 ATAACCTCTA
Statistics
Matches: 117, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 117 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (132 bp):
TGCTCACACGAGCTATGGGTCAAGATGTTAAGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
TCCGCAACCAATGCAAGACCTCAACCATCGGTAGAACATCTAAGACCAGCACCCATATAACTTGT
AA
Found at i:13978 original size:17 final size:17
Alignment explanation
Indices: 13956--13988 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13946 CATAAAGCAT
*
13956 AAAATAAACCAAAATAA
1 AAAATAAAACAAAATAA
13973 AAAATAAAACAAAATA
1 AAAATAAAACAAAATA
13989 TAAGTCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAATAAAACAAAATAA
Found at i:16103 original size:220 final size:219
Alignment explanation
Indices: 15696--16125 Score: 621
Period size: 220 Copynumber: 2.0 Consensus size: 219
15686 AATTTAAGGT
* *
15696 AATGTTCTTTTATTTTAGGGAATTCGAAAAGTGGTGCCCTAACGTGCTCGGTACAATTTTTTTTC
1 AATGTTATTTTATTTTAGGGAATTCGAAAAGTGGTGCCCTAACGTGCTCGGTACAATTTTTCTTC
* * * *
15761 AAACTTAAATAATCGAACATCCTATTTGAAATCGATAATCGCTATTTTTACTTGTAAATTACATG
66 AAACCTAAATAATCGAACATCATATTTAAAATCGATAATCGCCATTTTTACTTGTAAATTACATG
* * * *
15826 GGTATATCAATCTTTTTGCAAAGCATTTTTAACGAAATAAAATGTATATTATTTTTTAAATGCAT
131 GATATATCAATCTTTTTGCAAAACATTTTTAACAAAATAAAATGTATATTATTTTTTAAATACAT
15891 AAATTATTTTGAAAAAAATAAAAAC
196 AAATTATTTT-AAAAAAATAAAAAC
* * * *
15916 AATGTTATTTTATTTTAGGGAATTCGAAAAGTGGTGCTCTAACGTGTTGGGTACGATTTTTCTTC
1 AATGTTATTTTATTTTAGGGAATTCGAAAAGTGGTGCCCTAACGTGCTCGGTACAATTTTTCTTC
* * *
15981 GAACCTAAATAATCGAATATCATATTTAAAATCTATAATCGCCATTTTTACTTGTAAATTACATG
66 AAACCTAAATAATCGAACATCATATTTAAAATCGATAATCGCCATTTTTACTTGTAAATTACATG
* * * *
16046 GATTTATCCATC-TTTTGCAAAACGTTTTTAATAAAATAAAATGTATATCGT-TTTTTTAAATAC
131 GATATATCAATCTTTTTGCAAAACATTTTTAACAAAATAAAATGTATAT--TATTTTTTAAATAC
*
16109 ATAAATTGTTTTAAAAA
194 ATAAATTATTTTAAAAA
16126 TAAAGGTAAT
Statistics
Matches: 186, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
219 37 0.20
220 148 0.80
221 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (219 bp):
AATGTTATTTTATTTTAGGGAATTCGAAAAGTGGTGCCCTAACGTGCTCGGTACAATTTTTCTTC
AAACCTAAATAATCGAACATCATATTTAAAATCGATAATCGCCATTTTTACTTGTAAATTACATG
GATATATCAATCTTTTTGCAAAACATTTTTAACAAAATAAAATGTATATTATTTTTTAAATACAT
AAATTATTTTAAAAAAATAAAAAC
Found at i:16916 original size:158 final size:158
Alignment explanation
Indices: 16620--17022 Score: 583
Period size: 158 Copynumber: 2.6 Consensus size: 158
16610 TTCGACACTG
* * * *
16620 CTCACACGAGCTGTGGAGAATCCGCAACCAATGGAGGACCTCAGCCATCGGTAAGACGTCTAAGA
1 CTCACACGAGCTGTAGAGAATCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGA
* * * *
16685 CTAGCACCCATATAACCTATAATACTCACACGAGCTGTGAAATGGATCTGCTCACTCGAGCTGTG
66 CCAGCACCCATATAACCTGTAATACTCACACGAGCTGTGAAATGGACCTGCTCACACGAGCTGTG
*
16750 AGTTGAGATGTTAGGCTACACGATGCTA
131 AGTCGAGATGTTAGGCTACACGATGCTA
** * * *
16778 CTCACACGAGCTGTAGAGAATCTACAACCAATGCAAGACCTCAGTCATAGGTAGGACATCTAAGA
1 CTCACACGAGCTGTAGAGAATCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGA
*
16843 CCAGCACCCATATAACCTGTAATACTCACACGAGCAT-TGAAATGGGCCTGCTCACACGAGCTGT
66 CCAGCACCCATATAACCTGTAATACTCACACGAGC-TGTGAAATGGACCTGCTCACACGAGCTGT
* * *
16907 GGGTCGAGATGTTAGGCTACATGATGCTG
130 GAGTCGAGATGTTAGGCTACACGATGCTA
* * * *
16936 CTCACACGAGTTGTAGAGAATCCGCAACCAATGTAGGACCTCAGCCATCGATTGGACATCTAAGA
1 CTCACACGAGCTGTAGAGAATCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGA
*
17001 ACAGCACCCATATAACCTGTAA
66 CCAGCACCCATATAACCTGTAA
17023 ATAACCCCTA
Statistics
Matches: 216, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
158 215 1.00
159 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (158 bp):
CTCACACGAGCTGTAGAGAATCCGCAACCAATGCAGGACCTCAGCCATCGGTAGGACATCTAAGA
CCAGCACCCATATAACCTGTAATACTCACACGAGCTGTGAAATGGACCTGCTCACACGAGCTGTG
AGTCGAGATGTTAGGCTACACGATGCTA
Found at i:20717 original size:30 final size:32
Alignment explanation
Indices: 20665--20744 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 32
20655 TATCTATATC
*
20665 TTTATAATTTTTAAAAGATTAAA-T-TAAATT
1 TTTATTATTTTTAAAAGATTAAAGTGTAAATT
** * *
20695 TTTATTATTTTTAATGGGTTAAAGTGTAATTT
1 TTTATTATTTTTAAAAGATTAAAGTGTAAATT
*
20727 TTTTTTATTAATTTAAAA
1 TTTATTATT--TTTAAAA
20745 TTTTTTAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 19 0.50
31 1 0.03
32 13 0.34
34 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (32 bp):
TTTATTATTTTTAAAAGATTAAAGTGTAAATT
Found at i:20754 original size:15 final size:17
Alignment explanation
Indices: 20729--20760 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20719 TGTAATTTTT
20729 TTTTATTAA-TTTAAAA
1 TTTTATTAATTTTAAAA
20745 TTTT-TTAATTTTAAAA
1 TTTTATTAATTTTAAAA
20761 AATCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTATTAATTTTAAAA
Found at i:21084 original size:17 final size:17
Alignment explanation
Indices: 21057--21100 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
21047 GGTTATGCCC
*
21057 TAAAGTTTAATTTTTTTT
1 TAAA-TTTAATTTTTTTG
*
21075 TCAATTTAATTTTTTTG
1 TAAATTTAATTTTTTTG
21092 TAAATTTAA
1 TAAATTTAA
21101 ATTATGATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
TAAATTTAATTTTTTTG
Found at i:22124 original size:31 final size:30
Alignment explanation
Indices: 22058--22139 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
22048 AATGTGTAAT
*
22058 TGTATACAT-AAACTTTAATTTGGTGCAAA
1 TGTATACATGAAACTTTAATTTGATGCAAA
* * * *
22087 TATATACGTGAAACTCTAATTGTGATTCAAA
1 TGTATACATGAAACTTTAATT-TGATGCAAA
* *
22118 TGTATACTTGAAGCTTTAATTT
1 TGTATACATGAAACTTTAATTT
22140 TTATTTAAGC
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
29 7 0.17
30 11 0.26
31 24 0.57
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (30 bp):
TGTATACATGAAACTTTAATTTGATGCAAA
Found at i:23409 original size:12 final size:12
Alignment explanation
Indices: 23392--23416 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23382 ATTTCTTTTA
23392 AATAAAAATATC
1 AATAAAAATATC
23404 AATAAAAATATC
1 AATAAAAATATC
23416 A
1 A
23417 TGTAATGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAAATATC
Found at i:28055 original size:20 final size:20
Alignment explanation
Indices: 28030--28069 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28020 TAATGAAGGT
*
28030 ATGAGTTTTTATGCTATTAA
1 ATGAGTTTTGATGCTATTAA
28050 ATGAGTTTTGATGCTATTAA
1 ATGAGTTTTGATGCTATTAA
28070 TTTAACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47
Consensus pattern (20 bp):
ATGAGTTTTGATGCTATTAA
Done.