Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003531.1 Kokia drynarioides strain JFW-HI SEQ_116375, 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, 875
Length: 1459
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Found at i:1214 original size:29 final size:28
Alignment explanation
Indices: 1175--1428 Score: 119
Period size: 29 Copynumber: 8.7 Consensus size: 28
1165 AGCCCCATCA
*
1175 AAAATGGAATTTTTGAACATCTGAGGGT
1 AAAATGGAATTTTTGAACATTTGAGGGT
* *
1203 AAAATGGTAATTTTGGAAAATTTGA-GGT
1 AAAATGG-AATTTTTGAACATTTGAGGGT
* ** *
1231 CAAAAAAATGGAATTTTGGAAGGTTTGGGGGT
1 ----AAAATGGAATTTTTGAACATTTGAGGGT
* * *
1263 AAAAATGTAATTTTTAGAA-ATTTTAGTGTT
1 -AAAATGGAATTTTT-GAACATTTGAG-GGT
* *
1293 AAAGATGGAATTTTTGGACATTCGA-GGT
1 AAA-ATGGAATTTTTGAACATTTGAGGGT
* * *
1321 AAAATGATAATTTTGGAA-TTTTCG-GGGT
1 AAAATG-GAATTTTTGAACATTT-GAGGGT
* **
1349 CAAAAATGGAATTTTCGAACA-TCCAGGGT
1 --AAAATGGAATTTTTGAACATTTGAGGGT
1378 AAAATGGTAATTTTTGGAA-AGTTTG-GGGT
1 AAAATGG-AATTTTT-GAACA-TTTGAGGGT
*
1407 CAAAATTGGAATTTTTGGACAT
1 -AAAA-TGGAATTTTTGAACAT
1429 CTAGTAGTTA
Statistics
Matches: 171, Mismatches: 31, Indels: 47
0.69 0.12 0.19
Matches are distributed among these distances:
27 12 0.07
28 34 0.20
29 60 0.35
30 38 0.22
31 17 0.10
32 10 0.06
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGAACATTTGAGGGT
Found at i:1420 original size:30 final size:27
Alignment explanation
Indices: 1175--1425 Score: 116
Period size: 30 Copynumber: 8.6 Consensus size: 27
1165 AGCCCCATCA
*
1175 AAAATGGAATTTTT-GAACATCTGAGGGT
1 AAAATGGAATTTTTGGAA-ATTTG-GGGT
*
1203 AAAATGGTAA-TTTTGGAAAATTTGAGGT
1 AAAATGG-AATTTTTGG-AAATTTGGGGT
*
1231 CAAAAAAATGGAA-TTTTGGAAGGTTTGGGGGT
1 ----AAAATGGAATTTTTGGAA-ATTT-GGGGT
* * * *
1263 AAAAATGTAATTTTTAGAAATTTTAGTGTT
1 -AAAATGGAATTTTTGGAAA-TTT-GGGGT
* * *
1293 AAAGATGGAATTTTTGGACATTCGAGGT
1 AAA-ATGGAATTTTTGGAAATTTGGGGT
* *
1321 AAAAT-GATAATTTTGGAATTTTCGGGGT
1 AAAATGGA-ATTTTTGGAAATTT-GGGGT
* ***
1349 CAAAAATGGAA-TTTTCGAACATCCAGGGT
1 --AAAATGGAATTTTTGGAA-ATTTGGGGT
1378 AAAATGGTAATTTTTGGAAAGTTTGGGGT
1 AAAATGG-AATTTTTGGAAA-TTTGGGGT
1407 CAAAATTGGAATTTTTGGA
1 -AAAA-TGGAATTTTTGGA
1426 CATCTAGTAG
Statistics
Matches: 170, Mismatches: 30, Indels: 44
0.70 0.12 0.18
Matches are distributed among these distances:
26 2 0.01
27 19 0.11
28 27 0.16
29 44 0.26
30 51 0.30
31 16 0.09
32 11 0.06
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTTGGAAATTTGGGGT
Found at i:1420 original size:58 final size:58
Alignment explanation
Indices: 1172--1455 Score: 245
Period size: 57 Copynumber: 4.8 Consensus size: 58
1162 TGAAGCCCCA
* * *
1172 TCAAAAATGGAATTTTTGAACATCTGAGGGTAAAATGGTAA-TTTTGGAAAATTTGAGG
1 TCAAAAATGGAATTTTTGAACATC-CAGGGTAAAATGGTAATTTTTGGAAATTTTGGGG
* ** *** * * *
1230 TCAAAAAAATGGAATTTTGGAAGGTTTGGGGGTAAAAAT-GTAATTTTTAGAAATTTTAGTG
1 TC--AAAAATGGAATTTTTGAA-CATCCAGGGT-AAAATGGTAATTTTTGGAAATTTTGGGG
* * * * *
1291 TTAAAGATGGAATTTTTGGACATTC-GAGGTAAAATGATAA-TTTTGG-AATTTTCGGGG
1 TCAAAAATGGAATTTTTGAACATCCAG-GGTAAAATGGTAATTTTTGGAAATTTT-GGGG
* *
1348 TCAAAAATGGAATTTTCGAACATCCAGGGTAAAATGGTAATTTTTGGAAAGTTTGGGG
1 TCAAAAATGGAATTTTTGAACATCCAGGGTAAAATGGTAATTTTTGGAAATTTTGGGG
* * * * *
1406 TCAAAATTGGAATTTTTGGACATCTAGTAGTTAAATGGTAATTTTTGGAA
1 TCAAAAATGGAATTTTTGAACATCCAG-GGTAAAATGGTAATTTTTGGAA
1456 GGTT
Statistics
Matches: 180, Mismatches: 34, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
56 6 0.03
57 45 0.25
58 44 0.24
59 40 0.22
60 26 0.14
61 19 0.11
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGAACATCCAGGGTAAAATGGTAATTTTTGGAAATTTTGGGG
Done.