Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008179.1 Kokia drynarioides strain JFW-HI SEQ_122838, 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: 22064
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 47 characters in sequence are not A, C, G, or T
Found at i:1256 original size:2 final size:2
Alignment explanation
Indices: 1249--1275 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1239 CAGACAAGCT
1249 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 T
1276 GGAATAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7609 original size:70 final size:71
Alignment explanation
Indices: 7451--7610 Score: 214
Period size: 71 Copynumber: 2.3 Consensus size: 71
7441 ATAATTTATA
* * * * *
7451 ATAGCTATGGATATGTCAATAATTATGTAGATGGTGGTAATTTGTTGTCAATCTCTAATAATTTA
1 ATAGCTATGGATATGTCAACAATTATGTACATGATGGTAATTCGTTGTCAATCTATAATAATTTA
*
7516 AAATCG
66 AAATAG
* * * *
7522 ATAGCTATGGATGTGTCAACAGTTATTTCCATGATGGTAATTCGTTGTC-ATCTATAATAATTTA
1 ATAGCTATGGATATGTCAACAATTATGTACATGATGGTAATTCGTTGTCAATCTATAATAATTTA
*
7586 TAATAG
66 AAATAG
7592 ATAGCTATGGATATGTCAA
1 ATAGCTATGGATATGTCAA
7611 TAGTATAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
70 36 0.47
71 41 0.53
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (71 bp):
ATAGCTATGGATATGTCAACAATTATGTACATGATGGTAATTCGTTGTCAATCTATAATAATTTA
AAATAG
Found at i:16405 original size:21 final size:21
Alignment explanation
Indices: 16381--16421 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16371 TTCCATCACT
*
16381 AGAACTTGAATTTCCTCCACC
1 AGAACTTGAAGTTCCTCCACC
16402 AGAACTTGAAGTTCCTCCAC
1 AGAACTTGAAGTTCCTCCAC
16422 TAGGACTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (21 bp):
AGAACTTGAAGTTCCTCCACC
Found at i:20122 original size:21 final size:21
Alignment explanation
Indices: 20077--20123 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
20067 ACCATTACAC
* *
20077 AAAATAATATTTTAAATATCT
1 AAAATAATATTTAAAAAATCT
20098 -AAATAGATATTTAAAAAAT-T
1 AAAATA-ATATTTAAAAAATCT
20118 AAAATA
1 AAAATA
20124 CCACATGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATAATATTTAAAAAATCT
Found at i:21095 original size:29 final size:29
Alignment explanation
Indices: 21056--21275 Score: 214
Period size: 29 Copynumber: 7.6 Consensus size: 29
21046 ATTTAGGGTT
*
21056 TAAAAAT-GGATTTTTATACA-TTCGAGGG
1 TAAAAATGGGATTTTTAGA-AGTTCGAGGG
* *
21084 TAAAAATGGGATTTTTGGAAGTTTTG-GGG
1 TAAAAATGGGATTTTTAGAAG-TTCGAGGG
* * * *
21113 TCAAAATTGTGATTTTTGGAAGTTCGGGGG
1 T-AAAAATGGGATTTTTAGAAGTTCGAGGG
* * * *
21143 TCAAAATGGAATTTTTGGAAGTTTTG-GGG
1 TAAAAATGGGATTTTTAGAAG-TTCGAGGG
* *
21172 TTAAAAATGGAATTTTTGGAAGTTCGAGGG
1 -TAAAAATGGGATTTTTAGAAGTTCGAGGG
* *
21202 TAAAAATGGGATTTTTGGAAGTTCGGGGG
1 TAAAAATGGGATTTTTAGAAGTTCGAGGG
*
21231 TAAAAATGGGATTTTTAGAAGTTTGAGGG
1 TAAAAATGGGATTTTTAGAAGTTCGAGGG
*
21260 TAAAAATGGGAATTTT
1 TAAAAATGGGATTTTT
21276 GGATAGTTTA
Statistics
Matches: 165, Mismatches: 19, Indels: 15
0.83 0.10 0.08
Matches are distributed among these distances:
28 8 0.05
29 106 0.64
30 51 0.31
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
TAAAAATGGGATTTTTAGAAGTTCGAGGG
Found at i:21100 original size:59 final size:58
Alignment explanation
Indices: 21035--21288 Score: 296
Period size: 59 Copynumber: 4.3 Consensus size: 58
21025 TAAGATGGTA
* * *
21035 ATTTTTGGAAAATTTAGGGTTTAAAAATGGATTTTTATACA-TTCGAGGGTAAAAATGGG
1 ATTTTTGG-AAGTTTAGGGGTTAAAAATGGATTTTTAGA-AGTTCGAGGGTAAAAATGGG
* * * * * * *
21094 ATTTTTGGAAGTTTTGGGGTCAAAATTGTGATTTTTGGAAGTTCGGGGGTCAAAATGGA
1 ATTTTTGGAAGTTTAGGGGTTAAAAATG-GATTTTTAGAAGTTCGAGGGTAAAAATGGG
* *
21153 ATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGG
1 ATTTTTGGAAGTTTAGGGGTTAAAAATGG-ATTTTTAGAAGTTCGAGGGTAAAAATGGG
* * *
21212 ATTTTTGGAAG-TTCGGGGGTAAAAATGGGATTTTTAGAAGTTTGAGGGTAAAAATGGG
1 ATTTTTGGAAGTTTAGGGGTTAAAAAT-GGATTTTTAGAAGTTCGAGGGTAAAAATGGG
*
21270 AATTTTGGATAGTTTAGGG
1 ATTTTTGGA-AGTTTAGGG
21289 ACTTCCATGG
Statistics
Matches: 168, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
58 65 0.39
59 98 0.58
60 5 0.03
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (58 bp):
ATTTTTGGAAGTTTAGGGGTTAAAAATGGATTTTTAGAAGTTCGAGGGTAAAAATGGG
Found at i:21129 original size:30 final size:29
Alignment explanation
Indices: 21081--21284 Score: 241
Period size: 29 Copynumber: 6.9 Consensus size: 29
21071 ATACATTCGA
21081 GGGTAAAAATGGGATTTTTGGAAGTTTTG
1 GGGTAAAAATGGGATTTTTGGAAGTTTTG
* * **
21110 GGGTCAAAATTGTGATTTTTGGAAGTTCGG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTTG
* *
21140 GGGTCAAAATGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGGATTTTTGGAAGTTTTG
* *
21169 GGGTTAAAAATGGAATTTTTGGAAG-TTCG
1 GGG-TAAAAATGGGATTTTTGGAAGTTTTG
**
21198 AGGGTAAAAATGGGATTTTTGGAAGTTCGG
1 -GGGTAAAAATGGGATTTTTGGAAGTTTTG
*
21228 GGGTAAAAATGGGATTTTTAGAAG-TTTG
1 GGGTAAAAATGGGATTTTTGGAAGTTTTG
*
21256 AGGGTAAAAATGGGAATTTTGGATAGTTT
1 -GGGTAAAAATGGGATTTTTGGA-AGTTT
21285 AGGGACTTCC
Statistics
Matches: 148, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.01
29 92 0.62
30 52 0.35
31 2 0.01
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGGATTTTTGGAAGTTTTG
Done.