Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006225.1 Kokia drynarioides strain JFW-HI SEQ_120796, 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: 106016
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2126 original size:28 final size:27
Alignment explanation
Indices: 2061--2126 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
2051 AGAATGTAAG
*
2061 ATTATTTTGATAATAAAATTATGAGAAT
1 ATTATTTT-ATAATAAAATTATCAGAAT
2089 A-TATTATTATAGATAAAA-TATCAGATAT
1 ATTATT-TTATA-ATAAAATTATCAGA-AT
2117 ATTATTTTAT
1 ATTATTTTAT
2127 TTAATTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 13 0.39
28 16 0.48
29 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (27 bp):
ATTATTTTATAATAAAATTATCAGAAT
Found at i:2773 original size:20 final size:18
Alignment explanation
Indices: 2720--2774 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
2710 AAAAGGAATG
*
2720 TTAAATAAATATTTTTTTT
1 TTAAA-AAATATTTTTCTT
* *
2739 TTAAAAGAAAATTTTGGCTT
1 TTAAAA-AATATTTT-TCTT
2759 TTAAAAAATATTTTTC
1 TTAAAAAATATTTTTC
2775 CCTAATGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 8 0.28
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (18 bp):
TTAAAAAATATTTTTCTT
Found at i:23513 original size:36 final size:37
Alignment explanation
Indices: 23446--23515 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
23436 TAACCCAATC
* *
23446 TAAATTCAATTTAAATAATAAAATATATTTTTAAATT
1 TAAATTCAATTTAAAAAATAAAAAATATTTTTAAATT
*
23483 TAAATTTAA-TTAAAAAATAAATAAAT-TTTTTAA
1 TAAATTCAATTTAAAAAATAAA-AAATATTTTTAA
23516 TATTATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 18 0.62
37 11 0.38
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
TAAATTCAATTTAAAAAATAAAAAATATTTTTAAATT
Found at i:36443 original size:2 final size:2
Alignment explanation
Indices: 36436--36479 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
36426 TTAATGAACA
36436 AT AT 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 AT AT
36478 AT
1 AT
36480 GCAATTGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37216 original size:150 final size:150
Alignment explanation
Indices: 36940--37237 Score: 490
Period size: 150 Copynumber: 2.0 Consensus size: 150
36930 CACTCCCACC
* * *
36940 GATCGACTAACCATCTGTGACTAAGGATGTTCAAAAATACCCAACCCGAGATACCTGACTCGTTG
1 GATCGACTAACCATCTGTGACTAAGAATGTTAAAAAATACACAACCCGAGATACCTGACTCGTTG
37005 ACCCGTTAGTTTGAGCTTTTGTTTTCTATTTCACTATGTTGCTTTGCAAATCTTTTAGGTGATAG
66 ACCCGTTAGTTTGAGCTTTTGTTTTCTATTTCACTATGTTGCTTTGCAAATCTTTTAGGTGATAG
*
37070 AAAATTAGAAATTATGGACT
131 AAAATTAAAAATTATGGACT
* * * *
37090 GATCGACTGACCATCTGTGATTAAGAATGTTAAAAAATACACAACTCGAGATA-CTCGATTCGTT
1 GATCGACTAACCATCTGTGACTAAGAATGTTAAAAAATACACAACCCGAGATACCT-GACTCGTT
* *
37154 GACCCGTTAGTTTGAGCTTTTGTTTTCTATTTCACTATGTTGCTTTGTAAATCTTTTGGGTGATA
65 GACCCGTTAGTTTGAGCTTTTGTTTTCTATTTCACTATGTTGCTTTGCAAATCTTTTAGGTGATA
37219 GAAAATTAAAAATTATGGA
130 GAAAATTAAAAATTATGGA
37238 TATTTTATAA
Statistics
Matches: 137, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
149 2 0.01
150 135 0.99
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (150 bp):
GATCGACTAACCATCTGTGACTAAGAATGTTAAAAAATACACAACCCGAGATACCTGACTCGTTG
ACCCGTTAGTTTGAGCTTTTGTTTTCTATTTCACTATGTTGCTTTGCAAATCTTTTAGGTGATAG
AAAATTAAAAATTATGGACT
Found at i:37790 original size:21 final size:21
Alignment explanation
Indices: 37765--37811 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
37755 GAATGATGTA
37765 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* * *
37786 GTTTGGATTTCTAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
37807 ATTTG
1 ATTTG
37812 AATTATGCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:57143 original size:10 final size:10
Alignment explanation
Indices: 57120--57183 Score: 51
Period size: 10 Copynumber: 6.4 Consensus size: 10
57110 ATTCTAGATT
*
57120 TTTTTATTAA
1 TTTTTAATAA
57130 -TTTTAATAA
1 TTTTTAATAA
*
57139 TTTTTAACAA
1 TTTTTAATAA
*
57149 TTTCTT-ATCA
1 TTT-TTAATAA
* *
57159 TTCTTAATAG
1 TTTTTAATAA
57169 TTTTTAAATAA
1 TTTTT-AATAA
57180 TTTT
1 TTTT
57184 CTATGTTTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
9 10 0.24
10 21 0.51
11 10 0.24
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:70808 original size:16 final size:17
Alignment explanation
Indices: 70787--70820 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
70777 AAATATATAG
70787 ATTAAAA-TTTTAATGA
1 ATTAAAAGTTTTAATGA
70803 ATTAAAAGTTTTTAATGA
1 ATTAAAAG-TTTTAATGA
70821 TGCATAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
ATTAAAAGTTTTAATGA
Found at i:70979 original size:19 final size:19
Alignment explanation
Indices: 70957--71029 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
70947 TTAAATATAA
70957 ATTTTGATTTTTTATAAAT
1 ATTTTGATTTTTTATAAAT
* * * *
70976 ATTTTTAATTTTAAAAAATT
1 ATTTTGATTTTTTATAAA-T
*
70996 ATTTTGAATTTTTT-TATATT
1 ATTTTG-ATTTTTTATA-AAT
71016 ATTTTGATTATTTT
1 ATTTTGATT-TTTT
71030 GTAATTTTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
19 17 0.41
20 18 0.44
21 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTGATTTTTTATAAAT
Found at i:73438 original size:14 final size:15
Alignment explanation
Indices: 73404--73447 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
73394 CAAAAACATT
*
73404 TAAAATAATATATTAA
1 TAAAATAATA-ATTTA
73420 TAAAATAA-AATTTA
1 TAAAATAATAATTTA
73434 TAAAA-AATAATTTA
1 TAAAATAATAATTTA
73448 ATTTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 15 0.58
15 1 0.04
16 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATAATAATTTA
Found at i:83450 original size:20 final size:20
Alignment explanation
Indices: 83427--83464 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
83417 ATACATAACA
83427 TATTAATTATTATCATATAT
1 TATTAATTATTATCATATAT
* *
83447 TATTATTTATTATTATAT
1 TATTAATTATTATCATAT
83465 TGATTAAAAT
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:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTAATTATTATCATATAT
Found at i:83865 original size:16 final size:17
Alignment explanation
Indices: 83844--83876 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
83834 ATAATTATAG
83844 TATTAAA-AATATTTTA
1 TATTAAATAATATTTTA
83860 TATTAAATTAATATTTT
1 TATTAAA-TAATATTTT
83877 TAAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAAATAATATTTTA
Found at i:90377 original size:5 final size:5
Alignment explanation
Indices: 90364--90405 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
90354 GGTGAAAACT
*
90364 GAGAT GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GA
90406 AAAAAAACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (5 bp):
GAGAA
Found at i:95490 original size:4 final size:4
Alignment explanation
Indices: 95481--95509 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
95471 TCAGTTAATC
95481 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
95510 ACATGAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:95963 original size:17 final size:17
Alignment explanation
Indices: 95919--95963 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
95909 TTGAACATCC
95919 TTTGGTAGAATCATTCA
1 TTTGGTAGAATCATTCA
*
95936 TGATGG-AGAATCATTCA
1 T-TTGGTAGAATCATTCA
*
95953 TTTGGTTGAAT
1 TTTGGTAGAAT
95964 TTATCAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (17 bp):
TTTGGTAGAATCATTCA
Found at i:102356 original size:23 final size:23
Alignment explanation
Indices: 102324--102374 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
102314 CTCTAATAGA
*
102324 ATTTTTAAATTTTATAAATAAG-
1 ATTTTTAAATTTCATAAATAAGT
*
102346 ATTTTTGAAATTTCATTAATAAGT
1 ATTTTT-AAATTTCATAAATAAGT
102370 ATTTT
1 ATTTT
102375 ATAAGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 14 0.56
24 5 0.20
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (23 bp):
ATTTTTAAATTTCATAAATAAGT
Found at i:102407 original size:24 final size:26
Alignment explanation
Indices: 102371--102423 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
102361 TTAATAAGTA
*
102371 TTTTATAAGAATATA-AT-AAAATAT
1 TTTTATAAAAATATATATGAAAATAT
* *
102395 TTTTTTAAAAATATATATGATAATAT
1 TTTTATAAAAATATATATGAAAATAT
102421 TTT
1 TTT
102424 AAGATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 13 0.54
25 2 0.08
26 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTTATAAAAATATATATGAAAATAT
Found at i:103841 original size:16 final size:16
Alignment explanation
Indices: 103829--103862 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
103819 TAAATTTGAG
103829 TCCAAAAAAATTTAAA
1 TCCAAAAAAATTTAAA
* *
103845 TTCAAAAAAATTCAAA
1 TCCAAAAAAATTTAAA
103861 TC
1 TC
103863 TGACAGAAAT
Statistics
Matches: 15, Mismatches: 3, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
TCCAAAAAAATTTAAA
Done.