Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010055.1 Kokia drynarioides strain JFW-HI SEQ_124828, 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: 2621
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Found at i:25 original size:3 final size:3
Alignment explanation
Indices: 17--64 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
7 TAAGTTTAAC
* * * *
17 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAC AGT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
65 CATTAAACCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1263 original size:30 final size:30
Alignment explanation
Indices: 1227--1334 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
1217 CCCCAAAGGT
*
1227 CCCTAAACTATCCAAATATTATATTTTGAC
1 CCCTAAACTATCCAAATATTATATTTTAAC
1257 CCCTAAACT-TCTCTAAA-ATTATATTTTAAC
1 CCCTAAACTATC-C-AAATATTATATTTTAAC
* * * * * *
1287 ACCTAAACTTTTCAAAAATTACATTTTTAC
1 CCCTAAACTATCCAAATATTATATTTTAAC
* *
1317 CCCCAAACAATCCCAAAT
1 CCCTAAACTAT-CCAAAT
1335 TCCATTTTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
29 5 0.08
30 49 0.79
31 8 0.13
ACGTcount: A:0.39, C:0.26, G:0.01, T:0.34
Consensus pattern (30 bp):
CCCTAAACTATCCAAATATTATATTTTAAC
Found at i:1400 original size:57 final size:56
Alignment explanation
Indices: 1295--1724 Score: 440
Period size: 57 Copynumber: 7.5 Consensus size: 56
1285 ACACCTAAAC
* * * *
1295 TTTTCAAAAATTA-CATTTTTACCCCCAAACAATCCCAAATTCCATTTTTGACCTTGA
1 TTTTCCAAAATTACCA-TTTTACCCCCAAAC-TTCCAAAATTCCATTTTTGACCTCGA
* * *
1352 TTTTCCAAAAATTACCATTTTACCCCCGACCTTCCAAAATTCCATTTTTAACCTCGA
1 TTTTCC-AAAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTGACCTCGA
*
1409 TTTTTCCAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCGA
1 -TTTTCCAAAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGACCTCGA
* * *
1467 TTTTTCAAAATTACCATTTTACCCCCAAACTTCCAAGATTTTCATTTTT-ACCTCGA
1 TTTTCCAAAATTACCATTTTACCCCCAAACTTCCAA-AATTCCATTTTTGACCTCGA
* * *
1523 TTTTTCCAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCA-TTTTGACCCCGA
1 -TTTTCCAAAATTACCATTTTACCCCCAAAC-TTCCAAAATTCCATTTTTGACCTCGA
* *
1580 TTCTTCCCAAAATTACTATTTTACCCCCAAACTTCCAAAAACTT-CATTTTTTATCC-CGA
1 TT-TT-CCAAAATTACCATTTTACCCCCAAACTTCC-AAAA-TTCCATTTTTGA-CCTCGA
* * * * * * *
1639 TTCTTTCCAAAAATACCATTTTACCCTCGAA-TGCCTAAAATTTCATTTTTAACCTCAAA
1 -T-TTTCCAAAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGACCTC-GA
*
1698 CTTTCCCAAAATTACCATTTTACCCCC
1 -TTTTCCAAAATTACCATTTTACCCCC
1725 CGATACCCAA
Statistics
Matches: 320, Mismatches: 34, Indels: 37
0.82 0.09 0.09
Matches are distributed among these distances:
56 15 0.05
57 144 0.45
58 120 0.38
59 35 0.11
60 5 0.02
61 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (56 bp):
TTTTCCAAAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTGACCTCGA
Found at i:1605 original size:29 final size:29
Alignment explanation
Indices: 1350--1664 Score: 163
Period size: 29 Copynumber: 11.0 Consensus size: 29
1340 TTTTGACCTT
*
1350 GATT-TTCCAAAAATTACCATTTTACCCCC
1 GATTCTTCCCAAAATTACCATTTTA-CCCC
* *
1379 GA-CCTT-CCAAAATT-CCATTTTTAACCTC
1 GATTCTTCCCAAAATTACCA-TTTT-ACCCC
*
1407 GATT-TTTCCAAAATTACCATTTTACCCTC
1 GATTCTTCCCAAAATTACCATTTTACCC-C
** * *
1436 -AAACTTCCAAAAATT-CCATTTTTGACCTC
1 GATTCTTCCCAAAATTACCA-TTTT-ACCCC
*
1465 GATT-TT-TCAAAATTACCATTTTACCCC
1 GATTCTTCCCAAAATTACCATTTTACCCC
* ** * ** *
1492 CAAACTT-CCAAGATTTTCATTTTTACCTC
1 GATTCTTCCCAAAATTACCA-TTTTACCCC
*
1521 GATT-TTTCCAAAATTACCATTTTACCCC
1 GATTCTTCCCAAAATTACCATTTTACCCC
* ** * *
1549 TAAACTTTCCAAAATT-TCATTTTGACCCC
1 GATTCTTCCCAAAATTACCATTTT-ACCCC
*
1578 GATTCTTCCCAAAATTACTATTTTACCCC
1 GATTCTTCCCAAAATTACCATTTTACCCC
* ** * *
1607 CAAACTTCCAAAAACTT--CATTTTTTATCCC
1 GATTCTTCCCAAAA-TTACCA--TTTTACCCC
* *
1637 GATTCTTTCCAAAAATACCATTTTACCC
1 GATTCTTCCCAAAATTACCATTTTACCC
1665 TCGAATGCCT
Statistics
Matches: 210, Mismatches: 53, Indels: 46
0.68 0.17 0.15
Matches are distributed among these distances:
27 8 0.04
28 63 0.30
29 106 0.50
30 31 0.15
31 2 0.01
ACGTcount: A:0.30, C:0.29, G:0.03, T:0.38
Consensus pattern (29 bp):
GATTCTTCCCAAAATTACCATTTTACCCC
Done.