Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010580.1 Kokia drynarioides strain JFW-HI SEQ_125505, 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: 2132
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1192 original size:29 final size:28
Alignment explanation
Indices: 1150--1671 Score: 288
Period size: 29 Copynumber: 17.4 Consensus size: 28
1140 GGAGGTCCTT
*
1150 GAACTTCTAAAAATCACCATTTTACCCTC
1 GAACTTCCAAAAATCACCATTTTACCC-C
1179 GAACTTCCAAAAATC-CCATTTTTGACCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* * * *
1208 AAACCTTCTAAAGATTACCATTTTATCCCC
1 GAA-CTTCCAAAAATCACCATTTTA-CCCC
* *
1238 GAACATCCAAAAATC-TCATTTTTGACCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* * * *
1267 AAACTTTCCACAGATTACCATTTTACCCCC
1 GAAC-TTCCAAAAATCACCATTTTA-CCCC
*
1297 GAACTTCCAAAAATC-CCATTTTTGACCTC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* *
1326 GAACTTTCCAAAAATTACCATTTTACCTTC
1 GAAC-TTCCAAAAATCACCATTTTACC-CC
*
1356 GAACTTCCAAAAATC-CCATTTTTGACCTC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* * *
1385 GAACCTTCTAAAAATTATCATTTTACCCCC
1 GAA-CTTCCAAAAATCACCATTTTA-CCCC
*
1415 GAACTTCCAAAAATC-TCATTTTTGACCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* * *
1444 AAACCTTCTAAAAATTCTAAAATTTACCGTTTTACCCCCC
1 GAA-CTTCCAAAAA-TC--------ACCATTTTA--CCCC
*
1484 GAACTTCCAAAAGTC-CCATTTTTGACCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* * *
1513 AAACCTTCTAAAAATTACCATTTTATCCCC
1 GAA-CTTCCAAAAATCACCATTTTA-CCCC
* *
1543 GAACTTCCAAAAATC-TCATTTTTGATCCC
1 GAACTTCCAAAAATCACCA-TTTT-ACCCC
* *
1572 AAACTTTCCAAAAATTACCATTTTACCCTC
1 GAAC-TTCCAAAAATCACCATTTTACCC-C
*
1602 GAACTTCCAAAAAT--CCATTTTTTACCTCG
1 GAACTTCCAAAAATCACCA--TTTTACC-CC
* * *
1631 GATCTTCTAAAAATTACCATTTTACCCTC
1 GAACTTCCAAAAATCACCATTTTACCC-C
1660 GAACTTCCAAAA
1 GAACTTCCAAAA
1672 TCCTATTTTT
Statistics
Matches: 384, Mismatches: 58, Indels: 102
0.71 0.11 0.19
Matches are distributed among these distances:
27 3 0.01
28 17 0.04
29 182 0.47
30 139 0.36
31 21 0.05
38 3 0.01
39 12 0.03
40 7 0.02
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (28 bp):
GAACTTCCAAAAATCACCATTTTACCCC
Found at i:1247 original size:59 final size:58
Alignment explanation
Indices: 1153--1683 Score: 616
Period size: 59 Copynumber: 8.9 Consensus size: 58
1143 GGTCCTTGAA
*
1153 CTTCTAAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
1 CTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
* * *
1212 CTTCTAAAGATTACCATTTTATCCCCGAACATCCAAAAATCTCATTTTTGACCCCAAAC
1 CTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
* * * * * *
1271 TTTCCACAGATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAC
1 CTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
* * * * *
1330 TTTCCAAAAATTACCATTTTACCTTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAC
1 CTTCTAAAAATTACCATTTTACC-CCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
* *
1389 CTTCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAAC
1 CTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
* *
1448 CTTCTAAAAATTCTAAAATTTACCGTTTTACCCCCCGAACTTCCAAAAGTCCCATTTTTGACCCC
1 CTTCT----A----AAAA-TTACCATTTTA--CCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1513 AAAC
55 AAAC
* *
1517 CTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCTCATTTTTGATCCCAAAC
1 CTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
* * * * ** *
1576 TTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTTTACCTCGGAT
1 CTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
*
1634 CTTCTAAAAATTACCATTTTACCCTCGAACTTCC-AAAATCCTATTTTTGA
1 CTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGA
1684 TTCCGAACAT
Statistics
Matches: 413, Mismatches: 44, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
57 5 0.01
58 56 0.14
59 277 0.67
60 15 0.04
61 4 0.01
63 1 0.00
65 1 0.00
67 4 0.01
68 9 0.02
69 41 0.10
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (58 bp):
CTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAC
Done.