Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002835.1 Kokia drynarioides strain JFW-HI SEQ_115208, 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: 1884
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Found at i:379 original size:21 final size:23
Alignment explanation
Indices: 350--393 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
340 GGGGAAAATC
350 GTTTAGATCTAGG-CTAGATCTG
1 GTTTAGATCTAGGCCTAGATCTG
372 GTTT-GATCTAGGCCTAGATCTG
1 GTTTAGATCTAGGCCTAGATCTG
394 TTCTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (23 bp):
GTTTAGATCTAGGCCTAGATCTG
Found at i:1360 original size:58 final size:59
Alignment explanation
Indices: 1200--1580 Score: 511
Period size: 58 Copynumber: 6.5 Consensus size: 59
1190 CCCCGAAGGT
* * * *
1200 CCCCGAACTTCCAAAAATCCCAATTTTGACCTCGAACCTT-TCGAAAATTACCACTTTAC
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-AAAAATTACCATTTTAC
* * *
1259 CCTCGAACTTCCAAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTCAC
1 CCCCGAACTTCC-AAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
* *
1319 CCCCGAACTTCCAAAAAT-CCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTCAC
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
*
1377 CCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
* * ** * *
1436 CCCCTAACATCCAAAAATTTCA-TTTTGACCCCGAACATTTTAAAAATTACCATTTTAC
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
* * *
1494 CCCTGAACTT-CAAAAATCCCATTTTTGACCCTGAACCTT-TCAAAAATTACGATTTTAC
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-AAAAATTACCATTTTAC
* *
1552 CCTCGAACTTCCAAATATCCCATTTTTGA
1 CCCCGAACTTCCAAAAATCCCATTTTTGA
1581 GTTCGAACTT
Statistics
Matches: 289, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
57 10 0.03
58 138 0.48
59 90 0.31
60 50 0.17
61 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.30
Consensus pattern (59 bp):
CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
Found at i:1423 original size:117 final size:116
Alignment explanation
Indices: 1200--1580 Score: 500
Period size: 117 Copynumber: 3.2 Consensus size: 116
1190 CCCCGAAGGT
* * * *
1200 CCCCGAACTTCCAAAAATCCCAATTTTGACCTCGAACCTTTCGAAAATTACCACTTTACCCTCGA
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTT-AAAAATTACCA-TTTACCCCCGA
* *
1265 ACTTCCAAAAAATCCCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTCAC
64 ACTTCC-AAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
*
1319 CCCCGAACTTCCAAAAAT-CCATTTTTGACCCCAAACCTTCTAAAAATTACCATTTCACCCCCGA
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT-TAAAAATTACCATTT-ACCCCCGA
*
1383 ACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
64 ACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
* * ** * *
1436 CCCCTAACATCCAAAAATTTCA-TTTTGACCCCGAACATTTTAAAAATTACCATTTTACCCCTGA
1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC-CTTTAAAAATTACCA-TTTACCCCCGA
* *
1500 ACTT-CAAAAATCCCATTTTTGACCCTGAACCTT-TCAAAAATTACGATTTTAC
64 ACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCT-AAAAATTACCATTTTAC
* *
1552 CCTCGAACTTCCAAATATCCCATTTTTGA
1 CCCCGAACTTCCAAAAATCCCATTTTTGA
1581 GTTCGAACTT
Statistics
Matches: 232, Mismatches: 23, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
115 1 0.00
116 59 0.25
117 105 0.45
118 48 0.21
119 19 0.08
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.30
Consensus pattern (116 bp):
CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTAAAAATTACCATTTACCCCCGAAC
TTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATTACCATTTTAC
Found at i:1566 original size:29 final size:29
Alignment explanation
Indices: 1200--1614 Score: 268
Period size: 29 Copynumber: 14.2 Consensus size: 29
1190 CCCCGAAGGT
*
1200 CCCCGAACTTCCAAAAA-TCCCAATTTTGA
1 CCCCGAACTTCCAAAAATTACC-ATTTTGA
* * * *
1229 CCTCGAACCTTTCGAAAATTACCACTTT-A
1 CCCCGAA-CTTCCAAAAATTACCATTTTGA
* *
1258 CCCTCGAACTTCCAAAAAATCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATTACCA-TTTTGA
* * *
1289 CCCCAAACCTTCTAAAAATTACCA-TTTCA
1 CCCCGAA-CTTCCAAAAATTACCATTTTGA
1318 CCCCCGAACTTCCAAAAA-T-CCATTTTTGA
1 -CCCCGAACTTCCAAAAATTACCA-TTTTGA
* * *
1347 CCCCAAACCTTCTAAAAATTACCA-TTTCA
1 CCCCGAA-CTTCCAAAAATTACCATTTTGA
1376 CCCCCGAACTTCCAAAAA-T-CTCATTTTTGA
1 -CCCCGAACTTCCAAAAATTAC-CA-TTTTGA
*
1406 CCCCGAACCTTCTAAAAATTACCATTTT-A
1 CCCCGAA-CTTCCAAAAATTACCATTTTGA
* * *
1435 CCCCCTAACATCCAAAAATT-TCATTTTGA
1 -CCCCGAACTTCCAAAAATTACCATTTTGA
**
1464 CCCCGAACATTTTAAAAATTACCATTTT-A
1 CCCCGAAC-TTCCAAAAATTACCATTTTGA
*
1493 CCCCTGAACTT-CAAAAA-TCCCATTTTTGA
1 CCCC-GAACTTCCAAAAATTACCA-TTTTGA
* * *
1522 CCCTGAACCTTTCAAAAATTACGATTTT-A
1 CCCCGAA-CTTCCAAAAATTACCATTTTGA
* *
1551 CCCTCGAACTTCCAAATA-TCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATTACCA-TTTTGA
*** * *
1581 GTTCGAACTTTCC-AAAACTACCATTTTGC
1 CCCCGAAC-TTCCAAAAATTACCATTTTGA
1610 CCCCG
1 CCCCG
1615 TGCATCCGAA
Statistics
Matches: 298, Mismatches: 54, Indels: 68
0.71 0.13 0.16
Matches are distributed among these distances:
27 8 0.03
28 38 0.13
29 132 0.44
30 90 0.30
31 29 0.10
32 1 0.00
ACGTcount: A:0.33, C:0.32, G:0.06, T:0.30
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATTACCATTTTGA
Done.