Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002376.1 Kokia drynarioides strain JFW-HI SEQ_114456, 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: 5127
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:848 original size:3 final size:3
Alignment explanation
Indices: 840--864 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
830 TAAATAACAC
840 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
865 GTCTCAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1120 original size:30 final size:30
Alignment explanation
Indices: 1084--1143 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1074 AATTAGTAAA
*
1084 AATAAAATTATATTTTAA-CTTTTTAAAAAT
1 AATAAAATTATAATTTAATC-TTTTAAAAAT
*
1114 AATAAAATTTTAATTTAATCTTTTAAAAAT
1 AATAAAATTATAATTTAATCTTTTAAAAAT
1144 TACACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
AATAAAATTATAATTTAATCTTTTAAAAAT
Found at i:3146 original size:16 final size:16
Alignment explanation
Indices: 3125--3158 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3115 TTAAATGGTT
3125 ATTAATAATAATATTA
1 ATTAATAATAATATTA
*
3141 ATTAATATTAATATTA
1 ATTAATAATAATATTA
3157 AT
1 AT
3159 AAAAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAATAATAATATTA
Found at i:4335 original size:30 final size:30
Alignment explanation
Indices: 4273--4625 Score: 150
Period size: 30 Copynumber: 11.9 Consensus size: 30
4263 GAAGTCCCTG
** * ***
4273 AACTTTTTTAAAATCATATTTTAACTTTCA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
4303 AACTTTTCAAAAATCATATTTTGACCCCCA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* *
4333 AACATTTCAAAAAT--TCATTTTGA-CCCTA
1 AACTTTTCAAAAATCAT-ATTTTGACCCCCA
* * * * * *
4361 AACTTTTAAAAAATTACATTTTAACTCCTA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* * * * * *
4391 AACGTTCCAAAAATTCA-AATTTGGCTCCCG
1 AACTTTTCAAAAA-TCATATTTTGACCCCCA
* * * * **
4421 CACTTTTCAAAAATTACATTTTAACCCATA
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* *
4451 AACTTTTCAAAAATCATATTTTAACCCCCT
1 AACTTTTCAAAAATCATATTTTGACCCCCA
* * * **
4481 AAC-TTTCTAGAAATCACATTTTGA-CTCTT
1 AACTTTTC-AAAAATCATATTTTGACCCCCA
* * *
4510 AAC-TTTCAAAAAAAT-ACATTATGACCACCA
1 AACTTTTC--AAAAATCATATTTTGACCCCCA
** ** ** **
4540 AAC-TTTCCCAAATTTTAGAATTGACCCTTA
1 AACTTTTCAAAAATCATA-TTTTGACCCCCA
* *
4570 AACTTTTCAAAAATCATATTTTGACCTCCG
1 AACTTTTCAAAAATCATATTTTGACCCCCA
*
4600 ATC-TTTCTAAAAATCATATTTTGACC
1 AACTTTTC-AAAAATCATATTTTGACC
4626 TTGAACTTTC
Statistics
Matches: 239, Mismatches: 71, Indels: 26
0.71 0.21 0.08
Matches are distributed among these distances:
28 21 0.09
29 42 0.18
30 164 0.69
31 12 0.05
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (30 bp):
AACTTTTCAAAAATCATATTTTGACCCCCA
Found at i:4634 original size:29 final size:29
Alignment explanation
Indices: 4560--4653 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
4550 AATTTTAGAA
*
4560 TTGACCCTTAAACTTT-TCAAAAATCATATT
1 TTGA-CCTTGAACTTTCT-AAAAATCATATT
* *
4590 TTGACCTCCGATCTTTCTAAAAATCATATT
1 TTGACCT-TGAACTTTCTAAAAATCATATT
* * *
4620 TTGACCTTGAACTTTCCAAAATTCA-AAT
1 TTGACCTTGAACTTTCTAAAAATCATATT
4648 TTGACC
1 TTGACC
4654 CCAAACCTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.15
29 17 0.31
30 28 0.52
31 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (29 bp):
TTGACCTTGAACTTTCTAAAAATCATATT
Found at i:4711 original size:28 final size:28
Alignment explanation
Indices: 4570--4711 Score: 79
Period size: 28 Copynumber: 5.0 Consensus size: 28
4560 TTGACCCTTA
* * * *
4570 AACTTTTCAAAAATCATATTTTGACCTCCG
1 AACTTTCCAAAATTCA-ATTTTAACC-CTG
* * * * *
4600 ATCTTTCTAAAAATCATATTTTGACCTTG
1 AACTTTCCAAAATTCA-ATTTTAACCCTG
* * **
4629 AACTTTCCAAAATTCAAATTTGACCCCA
1 AACTTTCCAAAATTCAATTTTAACCCTG
* ** *
4657 AACCTTCC-AAATTTGATTTCAACCCCTG
1 AACTTTCCAAAATTCAATTTTAA-CCCTG
*
4685 AATTTTCCAAAATTCAATTTTAACCCT
1 AACTTTCCAAAATTCAATTTTAACCCT
4712 CAAAAGCCCC
Statistics
Matches: 85, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
27 9 0.11
28 28 0.33
29 25 0.29
30 23 0.27
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (28 bp):
AACTTTCCAAAATTCAATTTTAACCCTG
Found at i:4791 original size:17 final size:17
Alignment explanation
Indices: 4763--4815 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
4753 AAAATTCAAA
*
4763 TTTTTATCATTATTTAG
1 TTTTTTTCATTATTTAG
*
4780 TTTTTTTTATTATATTA-
1 TTTTTTTCATTAT-TTAG
*
4797 TATTTTTCATTATTT-G
1 TTTTTTTCATTATTTAG
4813 TTT
1 TTT
4816 GTTTAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.14
17 22 0.76
18 3 0.10
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (17 bp):
TTTTTTTCATTATTTAG
Done.