Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009482.1 Kokia drynarioides strain JFW-HI SEQ_124191, 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: 99514
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:8514 original size:58 final size:58
Alignment explanation
Indices: 8429--8585 Score: 251
Period size: 58 Copynumber: 2.7 Consensus size: 58
8419 AAAGGGATTG
* * ** * *
8429 TTTACGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTAA
1 TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAAAATTTGGGTTTAA
*
8487 TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAAAATTTGGGTTTAG
1 TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAAAATTTGGGTTTAA
8545 TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTA
1 TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTA
8586 GTTTGTTGAT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 92 1.00
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.48
Consensus pattern (58 bp):
TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAAAATTTGGGTTTAA
Found at i:29116 original size:21 final size:23
Alignment explanation
Indices: 29092--29136 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
29082 TTGTGTTAGC
29092 TCTACCGATACAAGT-ATG-ATT
1 TCTACCGATACAAGTCATGCATT
*
29113 TCTATCGATACAAGTCATGCATT
1 TCTACCGATACAAGTCATGCATT
29136 T
1 T
29137 ATTGATACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (23 bp):
TCTACCGATACAAGTCATGCATT
Found at i:39023 original size:52 final size:51
Alignment explanation
Indices: 38937--39233 Score: 317
Period size: 52 Copynumber: 5.7 Consensus size: 51
38927 ATTTCACTTC
* * * * * * * *
38937 ATTCATATACTCATGGTGACCCATAGCCACCGGA-CTTTATACTCAGTAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTA-A-TCCGTAAAGG
* ** *
38989 ATTCATATACTCTCGATGACACAGAGTCATCGGACCTCTTAATCCGTAAATG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCT-TTAATCCGTAAAGG
* * * *
39041 ATCCATATACTCACAATGACACTTAGTCATCAGACCGTTTAATTCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACC-TTTAATCCGTAAAGG
*
39093 ATTCATATACTCACGATGACACTTAGTCATCGGATCGTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGA-CCTTTAATCCGTAAAGG
* * * *
39145 ATTCATATACTCACGTTGACACTTAGTTATCGAACCTTTTAATCTGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACC-TTTAATCCGTAAAGG
* * *
39197 ATTCATATACTCATGATGACACTTAATCATTGGACCT
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCT
39234 CTTCGTTTAT
Statistics
Matches: 206, Mismatches: 34, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
51 2 0.01
52 196 0.95
53 5 0.02
54 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:48831 original size:20 final size:20
Alignment explanation
Indices: 48802--48839 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48792 GGTTTTTCGA
*
48802 AAAAAATCAATGGTCAACCC
1 AAAAAATCAATGATCAACCC
*
48822 AAAAAGTCAATGATCAAC
1 AAAAAATCAATGATCAAC
48840 GGGTCGAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.16
Consensus pattern (20 bp):
AAAAAATCAATGATCAACCC
Found at i:61761 original size:19 final size:18
Alignment explanation
Indices: 61739--61785 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 18
61729 ATTAAAATAT
61739 TTAATATATTTTAATTATG
1 TTAATATATTTT-ATTATG
61758 TTAAT-TA-TTTATTATG
1 TTAATATATTTTATTATG
61774 TTGAATAATATT
1 TT-AAT-ATATT
61786 ACTTCGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 2 0.08
19 7 0.29
20 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTAATATATTTTATTATG
Found at i:66184 original size:44 final size:44
Alignment explanation
Indices: 66134--66273 Score: 177
Period size: 44 Copynumber: 3.2 Consensus size: 44
66124 TTATAAGAGC
66134 AGACAAAAACTTTTAAAATTACTTATTAAAAAATAGAAAAACAA
1 AGACAAAAACTTTTAAAATTACTTATTAAAAAATAGAAAAACAA
66178 AGACAAAAACTTTTAAAATTAC-----AAAAAATAGAAAAACAAAGAA
1 AGACAAAAACTTTTAAAATTACTTATTAAAAAATAGAAAAAC----AA
66221 CAGACAAAAACTTTTAAAATTACTTATTAAAAAATA-AAAAACAA
1 -AGACAAAAACTTTTAAAATTACTTATTAAAAAATAGAAAAACAA
*
66265 ATA-AAAAAC
1 AGACAAAAAC
66274 GTAAAACTTA
Statistics
Matches: 85, Mismatches: 1, Indels: 22
0.79 0.01 0.20
Matches are distributed among these distances:
39 15 0.18
42 6 0.07
43 4 0.05
44 46 0.54
48 6 0.07
49 8 0.09
ACGTcount: A:0.64, C:0.10, G:0.04, T:0.21
Consensus pattern (44 bp):
AGACAAAAACTTTTAAAATTACTTATTAAAAAATAGAAAAACAA
Found at i:73945 original size:20 final size:20
Alignment explanation
Indices: 73906--73949 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
73896 TTAATTAAAA
*
73906 AAATGAGTATAATTTATGTT
1 AAATGAGTATAATTGATGTT
73926 AAATGAGTATAA-TGAGTGTT
1 AAATGAGTATAATTGA-TGTT
73946 AAAT
1 AAAT
73950 TAGTGCGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (20 bp):
AAATGAGTATAATTGATGTT
Found at i:76666 original size:24 final size:24
Alignment explanation
Indices: 76639--76691 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
76629 TTTCTAGAAG
* * *
76639 ATTTAGTATTTTTTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
* *
76663 ATTTTGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
76687 ATTTA
1 ATTTA
76692 ACTTACGTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:79599 original size:22 final size:23
Alignment explanation
Indices: 79563--79606 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
79553 AATTTGATTT
79563 ACTTTTAGTTACATTGACAATTA
1 ACTTTTAGTTACATTGACAATTA
79586 ACTTTTA-TTACATTGACAATT
1 ACTTTTAGTTACATTGACAATT
79607 TTAACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (23 bp):
ACTTTTAGTTACATTGACAATTA
Found at i:97039 original size:18 final size:17
Alignment explanation
Indices: 97016--97049 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
97006 TATTTAGTTG
97016 TCATTGCATTTTCATTTT
1 TCATTGCA-TTTCATTTT
97034 TCATTGCATTTCATTT
1 TCATTGCATTTCATTT
97050 GTTAGTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (17 bp):
TCATTGCATTTCATTTT
Found at i:97679 original size:17 final size:18
Alignment explanation
Indices: 97645--97686 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
97635 AAAATTTCAC
97645 AAGAAGAAAGAAAAAG-A
1 AAGAAGAAAGAAAAAGAA
*
97662 AAGAAGAATA-AAAGAGAA
1 AAGAAGAA-AGAAAAAGAA
97680 AAGAAGA
1 AAGAAGA
97687 GAAATGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (18 bp):
AAGAAGAAAGAAAAAGAA
Found at i:99237 original size:22 final size:23
Alignment explanation
Indices: 99194--99237 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
99184 AATTTGATTT
*
99194 ACTTTTAGTTACACTGATAATTA
1 ACTTTTAGTTACACTGACAATTA
*
99217 ACTTTTA-TTACATTGACAATT
1 ACTTTTAGTTACACTGACAATT
99238 TTAACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (23 bp):
ACTTTTAGTTACACTGACAATTA
Found at i:99484 original size:2 final size:2
Alignment explanation
Indices: 99477--99514 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
99467 TGCTACAATC
99477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.