Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008116.1 Kokia drynarioides strain JFW-HI SEQ_122774, 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: 16886
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5133 original size:18 final size:19
Alignment explanation
Indices: 5093--5133 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
5083 GGGCTTTTTG
* *
5093 TAATAACAAAAATAATAGA
1 TAATAACAAAAATAAAAAA
5112 -AATAAC-AAAATAAAAAA
1 TAATAACAAAAATAAAAAA
5129 TAATA
1 TAATA
5134 TTGGGAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (19 bp):
TAATAACAAAAATAAAAAA
Found at i:8407 original size:29 final size:29
Alignment explanation
Indices: 8364--8606 Score: 232
Period size: 29 Copynumber: 8.5 Consensus size: 29
8354 TATTTTCTTT
*
8364 AAAAATTACAATTTTGCCCTCAAACTTCC
1 AAAAATTACATTTTTGCCCTCAAACTTCC
** *
8393 AAAAATTATGTTTTTGCCCCCAAACTTCC
1 AAAAATTACATTTTTGCCCTCAAACTTCC
** *
8422 AAAAATTATGTTTTTGCCCTCAAATTTCTC
1 AAAAATTACATTTTTGCCCTCAAACTTC-C
8452 AAAAATTACA-TTTTG-CCTCGAAACTTCC
1 AAAAATTACATTTTTGCCCTC-AAACTTCC
* * *
8480 AAAAATCATATTTTTACCC-CAAACTTCTC
1 AAAAATTACATTTTTGCCCTCAAACTTC-C
**
8509 AAAAATTACATTTTTGCTCCT-AAACTTTT
1 AAAAATTACATTTTTGC-CCTCAAACTTCC
*
8538 AAAAATTACATTATTGCCC-C-AACTTCC
1 AAAAATTACATTTTTGCCCTCAAACTTCC
* **
8565 CAAAATTACATTTTACCCCT-AAACTTTCC
1 AAAAATTACATTTTTGCCCTCAAAC-TTCC
*
8594 -AAAATTACGTTTT
1 AAAAATTACATTTT
8607 AACCCGAACT
Statistics
Matches: 178, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
27 20 0.11
28 37 0.21
29 102 0.57
30 19 0.11
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTTGCCCTCAAACTTCC
Found at i:8760 original size:15 final size:15
Alignment explanation
Indices: 8736--8775 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
8726 TTCACGATTT
8736 GTAT-TTTATTTTTC
1 GTATATTTATTTTTC
*
8750 TTATATTTA-TTTTC
1 GTATATTTATTTTTC
8764 GTATATTTATTT
1 GTATATTTATTT
8776 ATTGGTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (15 bp):
GTATATTTATTTTTC
Found at i:13469 original size:29 final size:31
Alignment explanation
Indices: 13406--13665 Score: 190
Period size: 30 Copynumber: 8.7 Consensus size: 31
13396 CCCTAAATTG
* *
13406 TCAAAAAATCTCATTTTTAACACTAAAACTT
1 TCAAAAAATCTCATTTTTACCCCTAAAACTT
*
13437 TCAAAAAAAT-TTATTTTTACCCCT-AAAC-T
1 TC-AAAAAATCTCATTTTTACCCCTAAAACTT
* *
13466 TCAAAAAATCACATTTTTAACCCTAAAACTT
1 TCAAAAAATCTCATTTTTACCCCTAAAACTT
* **
13497 TCAAAAATTCT-ATTTTTA-CCCTCGAAC-T
1 TCAAAAAATCTCATTTTTACCCCTAAAACTT
* *
13525 TCTAAAAATCCCATTTTTAACCCC-AAAACTT
1 TCAAAAAATCTCATTTTT-ACCCCTAAAACTT
* * *
13556 TCAAAAATTAT-ATTTTTACCCC--GAAC-T
1 TCAAAAAATCTCATTTTTACCCCTAAAACTT
* * * * *
13583 TCCAAAAATCCCATTTTAACCTC-GAAACTT
1 TCAAAAAATCTCATTTTTACCCCTAAAACTT
* *
13613 TCAAAAATTCT-ATTTTTACCTCC-CAAACTT
1 TCAAAAAATCTCATTTTTACC-CCTAAAACTT
*
13643 TC-AAAAATCCCATTTTTGACCCC
1 TCAAAAAATCTCATTTTT-ACCCC
13666 GAATTTTCCC
Statistics
Matches: 180, Mismatches: 35, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
27 8 0.04
28 28 0.16
29 49 0.27
30 51 0.28
31 37 0.21
32 7 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (31 bp):
TCAAAAAATCTCATTTTTACCCCTAAAACTT
Found at i:13515 original size:59 final size:59
Alignment explanation
Indices: 13396--13664 Score: 316
Period size: 59 Copynumber: 4.5 Consensus size: 59
13386 TCCCGTAAGT
* * *
13396 CCCTAAATTGTCAAAAAATCTCATTTTTAACACTAAAACTTTCAAAAAAATT-TATTTTTAC
1 CCCTAAACT-TCAAAAAATCCCATTTTTAACCCTAAAACTTTC--AAAAATTCTATTTTTAC
*
13457 CCCTAAACTTCAAAAAATCACATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTA-
1 CCCTAAACTTCAAAAAATCCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTAC
* * * *
13515 CCCTCGAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAATTATATTTTTAC
1 CCCT-AAACTTCAAAAAATCCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTAC
* * *
13575 CCC-GAACTTCCAAAAATCCCA-TTTTAA-CCTCGAAACTTTCAAAAATTCTATTTTTAC
1 CCCTAAACTTCAAAAAATCCCATTTTTAACCCT-AAAACTTTCAAAAATTCTATTTTTAC
* *
13632 CTCCCAAACTTTC-AAAAATCCCATTTTTGACCC
1 C-CCTAAAC-TTCAAAAAATCCCATTTTTAACCC
13665 CGAATTTTCC
Statistics
Matches: 185, Mismatches: 14, Indels: 18
0.85 0.06 0.08
Matches are distributed among these distances:
56 2 0.01
57 31 0.17
58 30 0.16
59 70 0.38
60 42 0.23
61 10 0.05
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (59 bp):
CCCTAAACTTCAAAAAATCCCATTTTTAACCCTAAAACTTTCAAAAATTCTATTTTTAC
Found at i:13673 original size:29 final size:28
Alignment explanation
Indices: 13449--13673 Score: 175
Period size: 29 Copynumber: 7.7 Consensus size: 28
13439 AAAAAAATTT
* *
13449 ATTTTTACCCCTAAAC-TTCAAAAAATCAC
1 ATTTTTACCCC-GAACTTTC-AAAAATCCC
** * *
13478 ATTTTTAACCCTAAAACTTTCAAAAATTCT
1 ATTTTT-ACCC-CGAACTTTCAAAAATCCC
13508 ATTTTTACCCTCGAAC-TTCTAAAAATCCC
1 ATTTTTACCC-CGAACTTTC-AAAAATCCC
* ***
13537 ATTTTTAACCCCAAAACTTTCAAAAATTAT
1 ATTTTT-ACCCC-GAACTTTCAAAAATCCC
*
13567 ATTTTTACCCCGAACTTCCAAAAATCCC
1 ATTTTTACCCCGAACTTTCAAAAATCCC
* * * *
13595 ATTTTAACCTCGAAACTTTCAAAAATTCT
1 ATTTTTACCCCG-AACTTTCAAAAATCCC
*
13624 ATTTTTACCTCCCAAACTTTCAAAAATCCC
1 ATTTTTA-C-CCCGAACTTTCAAAAATCCC
*
13654 ATTTTTGACCCCGAATTTTC
1 ATTTTT-ACCCCGAACTTTC
13674 CCAAAATTAT
Statistics
Matches: 156, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
28 25 0.16
29 61 0.39
30 61 0.39
31 9 0.06
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (28 bp):
ATTTTTACCCCGAACTTTCAAAAATCCC
Found at i:13746 original size:29 final size:29
Alignment explanation
Indices: 13691--13747 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
13681 TATCGTTTCA
*
13691 CCCCGAGAATCTAAAATTATCACTTTTGC
1 CCCCGAGAATCTAAAAGTATCACTTTTGC
* *
13720 CCCCGAGAATTTGAAAAGTCTCA-TTTTG
1 CCCCGAGAATCT-AAAAGTATCACTTTTG
13748 AACTCCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (29 bp):
CCCCGAGAATCTAAAAGTATCACTTTTGC
Done.