Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010281.1 Kokia drynarioides strain JFW-HI SEQ_125128, 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: 5794
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:332 original size:16 final size:17
Alignment explanation
Indices: 300--334 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
290 ATCATGAAAT
300 ATTAATAATAAATAAAA
1 ATTAATAATAAATAAAA
*
317 ATTAAT-ATATATAAAA
1 ATTAATAATAAATAAAA
333 AT
1 AT
335 GTATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAATAATAAATAAAA
Found at i:1307 original size:29 final size:29
Alignment explanation
Indices: 1253--1671 Score: 213
Period size: 29 Copynumber: 14.4 Consensus size: 29
1243 AAACTTTTTT
* *
1253 AAAATTATATTTTAACCTCTAAACTTCTCA
1 AAAATTACATTTTTACCTC-AAACTTCTCA
* **
1283 AAAATTACACTTTTACCTTGAACTT-TCTA
1 AAAATTACATTTTTACCTCAAACTTCTC-A
* * *
1312 AAAATTACATTTTTGCCCCTAAACTT-TTA
1 AAAATTACATTTTTACCTC-AAACTTCTCA
1341 AAAATTACATTTTTACCTCCAAACTTC-CA
1 AAAATTACATTTTTACCT-CAAACTTCTCA
*
1370 AAAATCACATTTTTACCCTCAAACTTC-CA
1 AAAATTACATTTTTA-CCTCAAACTTCTCA
* * * * *
1399 AAAATCATATTTTTGCCCCCGAACTT-TCA
1 AAAATTACATTTTT-ACCTCAAACTTCTCA
* * *
1428 AAAATTATATTTTTTACCCCTAAACTACT--
1 AAAATTACA-TTTTTACCTC-AAACTTCTCA
* * * * * *
1457 AAAATCACCTATTTACCCCCGAACTT-GCA
1 AAAATTACATTTTTA-CCTCAAACTTCTCA
* * * *
1486 AATATCACATTTTTACCCTCGATCTTC-CA
1 AAAATTACATTTTTA-CCTCAAACTTCTCA
*
1515 AAAATTACATTTTT-CCCCTAAACTTC-CA
1 AAAATTACATTTTTACCTC-AAACTTCTCA
* * *
1543 AAAATCATATTTTTACC-CTAAACTTCTCC
1 AAAATTACATTTTTACCTC-AAACTTCTCA
* * * *
1572 AAAATCACTTTTTTACCCCAAAC-TCTCCC
1 AAAATTACATTTTTACCTCAAACTTCT-CA
* * *
1601 AAAATGACATTTTTACCCTTAAAACTT-TCC
1 AAAATTACATTTTTA-CC-TCAAACTTCTCA
* *
1631 AAAATTACATTTTCACCCCAAAC-TCTCCA
1 AAAATTACATTTTTACCTCAAACTTCT-CA
*
1660 AAACTT-CATTTT
1 AAAATTACATTTT
1672 AAACCTCATT
Statistics
Matches: 310, Mismatches: 55, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
27 4 0.01
28 53 0.17
29 194 0.63
30 52 0.17
31 6 0.02
32 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCTCAAACTTCTCA
Found at i:1384 original size:87 final size:87
Alignment explanation
Indices: 1253--1648 Score: 331
Period size: 87 Copynumber: 4.5 Consensus size: 87
1243 AAACTTTTTT
* * * * * *
1253 AAAATTATATTTTAACCTCTAAACTTCTCAAAAATTACACTTTTA-CCTTGAACTTTCTAAAAAT
1 AAAATTACATTTTTACCCCTAAACTTC-CAAAAATCACATTTTTACCCTCGAACTTTC-AAAAAT
* *
1317 TACATTTTTGCCCCTAAACTTTTA
64 CACATTTTTGCCCCTAAACTTTCA
* *
1341 AAAATTACATTTTTACCTCC-AAACTTCCAAAAATCACATTTTTACCCTCAAACTTCCAAAAATC
1 AAAATTACATTTTTACC-CCTAAACTTCCAAAAATCACATTTTTACCCTCGAACTTTCAAAAATC
* **
1405 ATATTTTTGCCCCCGAACTTTCA
65 ACATTTTTGCCCCTAAACTTTCA
* * * * * * * *
1428 AAAATTATATTTTTTACCCCTAAAC-TACTAAAATCACCTATTTACCCCCGAACTTGCAAATATC
1 AAAATTACA-TTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCTCGAACTTTCAAAAATC
* * * *
1492 ACATTTTT-ACCCTCGATCTTCCA
65 ACATTTTTGCCCCT-AAACTTTCA
* * *
1515 AAAATTACATTTTT-CCCCTAAACTTCCAAAAATCATATTTTTACCCT-AAACTTCTCCAAAATC
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCTCGAACTT-TCAAAAATC
* * * *
1578 ACTTTTTTACCCC-AAACTCTCCC
65 ACATTTTTGCCCCTAAACT-TTCA
* * * *
1601 AAAATGACATTTTTACCCTTAAAACTTTCC-AAAATTACATTTTCACCC
1 AAAATTACATTTTTACCCCT-AAAC-TTCCAAAAATCACATTTTTACCC
1649 CAAACTCTCC
Statistics
Matches: 248, Mismatches: 48, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
85 17 0.07
86 54 0.22
87 110 0.44
88 62 0.25
89 5 0.02
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (87 bp):
AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCTCGAACTTTCAAAAATCA
CATTTTTGCCCCTAAACTTTCA
Found at i:2089 original size:97 final size:97
Alignment explanation
Indices: 1923--2113 Score: 292
Period size: 97 Copynumber: 2.0 Consensus size: 97
1913 AAAATATTCA
* * * **
1923 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGCCGTGAT
1 AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCCTAACTTACTAGCCACGAT
* *
1988 TTTTCTTCAAACCGGGATAATCGAATACCCTT
66 TTTTCTTCAAACCAGGAAAATCGAATACCCTT
* *
2020 AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAATTTTTGCCCTAACTTACTAGGCACGAT
1 AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCCTAACTTACTAGCCACGAT
*
2085 TTTTCTTCAAACCAGGAAAATTGAATACC
66 TTTTCTTCAAACCAGGAAAATCGAATACC
2114 TTTTTTTCAA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (97 bp):
AAATCGAGGAAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCCTAACTTACTAGCCACGAT
TTTTCTTCAAACCAGGAAAATCGAATACCCTT
Done.