Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006090.1 Kokia drynarioides strain JFW-HI SEQ_120585, 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: 40512
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1136 original size:20 final size:20
Alignment explanation
Indices: 1088--1142 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1078 TTAGCCATTC
*
1088 TTTTTATTTTTATTTTATTA
1 TTTTTATTTTTATTTAATTA
**
1108 TTTGCATTTTTAATTTAATT-
1 TTTTTATTTTT-ATTTAATTA
1128 TTTTTA-TTTTATTTA
1 TTTTTATTTTTATTTA
1143 TTTCCTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 13 0.45
21 7 0.24
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTTATTTAATTA
Found at i:3943 original size:6 final size:6
Alignment explanation
Indices: 3932--4052 Score: 91
Period size: 6 Copynumber: 19.2 Consensus size: 6
3922 TTATTACATG
* *
3932 TATTTT TATTTT CATTTTT TAATTTT TAATTTT TAATTTT TCATTTT CATTTT
1 TATTTT TATTTT TA-TTTT T-ATTTT T-ATTTT T-ATTTT T-ATTTT TATTTT
* * * * * * *
3985 CATTTT TCTTTT CATTTT TAGTTT TAGTTT TAGTTT TAGTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
4033 TAGTTTAT T-TTTT TATTTT T
1 TA-TTT-T TATTTT TATTTT T
4053 TTATTATGCA
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
5 2 0.02
6 63 0.64
7 31 0.31
8 3 0.03
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:3957 original size:7 final size:7
Alignment explanation
Indices: 3933--3978 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
3923 TATTACATGT
3933 ATTTTT-
1 ATTTTTA
*
3939 ATTTTCA
1 ATTTTTA
*
3946 TTTTTTA
1 ATTTTTA
3953 ATTTTTA
1 ATTTTTA
3960 ATTTTTA
1 ATTTTTA
*
3967 ATTTTTC
1 ATTTTTA
3974 ATTTT
1 ATTTT
3979 CATTTTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:3991 original size:7 final size:7
Alignment explanation
Indices: 3940--4003 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
3930 TGTATTTTTA
3940 TTTTCATT
1 TTTTCA-T
*
3948 TTTTAAT
1 TTTTCAT
*
3955 TTTTAAT
1 TTTTCAT
*
3962 TTTTAAT
1 TTTTCAT
3969 TTTTCA-
1 TTTTCAT
3975 TTTTCA-
1 TTTTCAT
3981 TTTTCAT
1 TTTTCAT
3988 TTTTC--
1 TTTTCAT
3993 TTTTCAT
1 TTTTCAT
4000 TTTT
1 TTTT
4004 AGTTTTAGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.10
6 12 0.24
7 29 0.57
8 5 0.10
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTCAT
Found at i:3996 original size:18 final size:19
Alignment explanation
Indices: 3962--4002 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3952 AATTTTTAAT
3962 TTTTAATTTTTCATTTTCA
1 TTTTAATTTTTCATTTTCA
*
3981 TTTTCATTTTTC-TTTTCA
1 TTTTAATTTTTCATTTTCA
3999 TTTT
1 TTTT
4003 TAGTTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTAATTTTTCATTTTCA
Found at i:10132 original size:14 final size:14
Alignment explanation
Indices: 10109--10159 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
10099 TAAGGAGAGT
*
10109 GAGAGTGAGGAAGA
1 GAGAGAGAGGAAGA
*
10123 GAGAGAGAGGAGGA
1 GAGAGAGAGGAAGA
* *
10137 GGGAGGGAGGAAGA
1 GAGAGAGAGGAAGA
10151 GAGAGAGAG
1 GAGAGAGAG
10160 AAACCCGATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.57, T:0.02
Consensus pattern (14 bp):
GAGAGAGAGGAAGA
Found at i:18623 original size:26 final size:26
Alignment explanation
Indices: 18541--18639 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 26
18531 AATGTCACTG
* * *
18541 CATGAGCATGTCTAGAATTGTCGTTG
1 CATGAACATGTCCAGAATTGTCGTTA
** * * *
18567 CAAAAACTTGTCCAGAATTATCGTTG
1 CATGAACATGTCCAGAATTGTCGTTA
*
18593 CATGAACATGTCCAGAGTTGTCGTTA
1 CATGAACATGTCCAGAATTGTCGTTA
* * *
18619 TATGAGCATGTCGAGAATTGT
1 CATGAACATGTCCAGAATTGT
18640 GCCTAAAATT
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (26 bp):
CATGAACATGTCCAGAATTGTCGTTA
Found at i:22367 original size:18 final size:20
Alignment explanation
Indices: 22333--22369 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
22323 TGTAAAAAAA
22333 TTTTGCTTTTCTCTTCTTTG
1 TTTTGCTTTTCTCTTCTTTG
22353 TTTT-CTTTT-TCTTCTTT
1 TTTTGCTTTTCTCTTCTTT
22370 TCTATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTGCTTTTCTCTTCTTTG
Found at i:22998 original size:18 final size:17
Alignment explanation
Indices: 22960--23003 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
22950 AAATGTACTA
* *
22960 ACAAATAAAATGCATTT
1 ACAAATAAAATGCAATG
22977 ACAAATAAAAGTGCAATG
1 ACAAATAAAA-TGCAATG
*
22995 ACAACTAAA
1 ACAAATAAA
23004 TGCTATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (17 bp):
ACAAATAAAATGCAATG
Found at i:23158 original size:18 final size:18
Alignment explanation
Indices: 23120--23158 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23110 CTGTTTTGCG
* *
23120 CCTCTTTTTCTTGTCTTT
1 CCTCTTTCTCTTGTCTGT
*
23138 CCTCTTTCTCTTTTCTGT
1 CCTCTTTCTCTTGTCTGT
23156 CCT
1 CCT
23159 TGGAATCGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.62
Consensus pattern (18 bp):
CCTCTTTCTCTTGTCTGT
Found at i:24517 original size:52 final size:52
Alignment explanation
Indices: 24439--24542 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
24429 TAGATCTAGC
*
24439 ATCACCAGGTTAGCACCTTCATCAGTTAACTCCTCTAAAAACGCAGTGTAGG
1 ATCACCAGGTTAGCACATTCATCAGTTAACTCCTCTAAAAACGCAGTGTAGG
24491 ATCACCAGGTTAGCACATTCATCAGTTAACTCCTCTAAAAACGCAGTGTAGG
1 ATCACCAGGTTAGCACATTCATCAGTTAACTCCTCTAAAAACGCAGTGTAGG
24543 TATCTTCCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (52 bp):
ATCACCAGGTTAGCACATTCATCAGTTAACTCCTCTAAAAACGCAGTGTAGG
Found at i:28402 original size:16 final size:17
Alignment explanation
Indices: 28366--28404 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28356 TATCAAAATG
28366 AATGCAGTGACAATAAA
1 AATGCAGTGACAATAAA
28383 AATGCAG-GCACAAT-AA
1 AATGCAGTG-ACAATAAA
28399 AATGCA
1 AATGCA
28405 AGAATGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AATGCAGTGACAATAAA
Found at i:31518 original size:21 final size:20
Alignment explanation
Indices: 31463--31518 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
31453 TTAGTTCGGT
*
31463 TATTTATATTA-TATTATTTC
1 TATTTA-ATTATTATTTTTTC
*
31483 TATTT-ATTTTTATTTTTTC
1 TATTTAATTATTATTTTTTC
31502 TATTTTAATTATTATTT
1 TA-TTTAATTATTATTT
31519 ATTAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 8 0.27
21 9 0.30
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTAATTATTATTTTTTC
Found at i:31530 original size:25 final size:24
Alignment explanation
Indices: 31469--31532 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
31459 CGGTTATTTA
*
31469 TATTATATTATTTCTATTTATT-TT
1 TATTATATTATTT-TAATTATTATT
* *
31493 TATTTTTTCTATTTTAATTATTATT
1 TATTATAT-TATTTTAATTATTATT
31518 TATTAATATTATTTT
1 TATT-ATATTATTTT
31533 TATTTTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 13 0.41
25 17 0.53
26 2 0.06
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTATATTATTTTAATTATTATT
Found at i:35059 original size:23 final size:23
Alignment explanation
Indices: 35029--35087 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
35019 TCTGACTGGC
35029 ATCCAGTCAACAACTTCTAGAAG
1 ATCCAGTCAACAACTTCTAGAAG
* *
35052 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAACAACTTCTAGAAG
*
35075 -GCCTAGTCAACAA
1 ATCC-AGTCAACAA
35088 GGATGGACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (23 bp):
ATCCAGTCAACAACTTCTAGAAG
Found at i:36493 original size:80 final size:80
Alignment explanation
Indices: 36380--36548 Score: 214
Period size: 80 Copynumber: 2.1 Consensus size: 80
36370 GGATTAACAA
* *
36380 ACAAATATTCGTCAAATCTAAACACCTAGTGCTTAGCTGATAAGCCACAAATGTAAGCCCAGCTC
1 ACAAATATTCGTCAAATCTAAACACCTAGTGCTTAGCGGATAAACCACAAATGTAAGCCCAGCTC
*
36445 TAGTCGGTTAAACCG
66 TAGTCAGTTAAACCG
* * * ** * *
36460 ACAAATATTTGTCAAATCTTAGCA-CTCAGTGCTTAGCGGATAAACTGCAAATGTGAGCCCATCT
1 ACAAATATTCGTCAAATCTAAACACCT-AGTGCTTAGCGGATAAACCACAAATGTAAGCCCAGCT
*
36524 CTAGTCAGTTAAACTG
65 CTAGTCAGTTAAACCG
36540 ACAACATAT
1 ACAA-ATAT
36549 ATTCATCAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
79 2 0.03
80 70 0.92
81 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (80 bp):
ACAAATATTCGTCAAATCTAAACACCTAGTGCTTAGCGGATAAACCACAAATGTAAGCCCAGCTC
TAGTCAGTTAAACCG
Done.