Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003420.1 Kokia drynarioides strain JFW-HI SEQ_116187, 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: 27079
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:801 original size:39 final size:38
Alignment explanation
Indices: 671--800 Score: 135
Period size: 39 Copynumber: 3.4 Consensus size: 38
661 TATATTGGGT
* *
671 TTTGTT-TTTGGTTTTTTGAA-GATGATGGGTTC--TTTG
1 TTTGTTATTT-GTTTTTTGAATG-TGCTGAGTTCTTTTTG
* * *
707 TTTATTATTTGTTCTTTGAATGTGCTGAGTTCTTTATTA
1 TTTGTTATTTGTTTTTTGAATGTGCTGAGTTCTTT-TTG
*
746 TTTGTTATTTGTTTTTTGAATGTGTTGAGTT-TTTTTG
1 TTTGTTATTTGTTTTTTGAATGTGCTGAGTTCTTTTTG
783 TTTGTTATTTGCTTTTTT
1 TTTGTTATTTG-TTTTTT
801 TTTATGGAGT
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
36 22 0.28
37 17 0.22
38 10 0.13
39 30 0.38
ACGTcount: A:0.12, C:0.04, G:0.20, T:0.64
Consensus pattern (38 bp):
TTTGTTATTTGTTTTTTGAATGTGCTGAGTTCTTTTTG
Found at i:1552 original size:22 final size:23
Alignment explanation
Indices: 1527--1572 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1517 TGGGGTGATT
1527 TTTTTTAA-TATTAATATAATTA
1 TTTTTTAATTATTAATATAATTA
* *
1549 -TTTTTAATTATTATTATTATTA
1 TTTTTTAATTATTAATATAATTA
1571 TT
1 TT
1573 ATAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
21 7 0.35
22 12 0.60
23 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTTAATTATTAATATAATTA
Found at i:2099 original size:21 final size:22
Alignment explanation
Indices: 2068--2108 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2058 ATAAATATTA
*
2068 AAAATTTAAAAAAATCTAAACT
1 AAAATTTAAAAAAATATAAACT
2090 AAAA-TTAAAAAAATATAAA
1 AAAATTTAAAAAAATATAAA
2109 AGTTCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATTTAAAAAAATATAAACT
Found at i:4077 original size:17 final size:18
Alignment explanation
Indices: 4047--4083 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4037 CAAATAACTC
4047 AAAAATCATAAAAATTAA
1 AAAAATCATAAAAATTAA
*
4065 AAAAAT-ATCAAAATTAA
1 AAAAATCATAAAAATTAA
4082 AA
1 AA
4084 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
AAAAATCATAAAAATTAA
Found at i:7118 original size:32 final size:32
Alignment explanation
Indices: 7045--7108 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
7035 AAAAAGAGTC
*
7045 AAATCGTTTTTT--AACAAAAATGATAATTAAA
1 AAAT-GTTTTTTAAAACAAAAACGATAATTAAA
7076 AAATGTTTTTTAAAACAAAAACGATAATTAAA
1 AAATGTTTTTTAAAACAAAAACGATAATTAAA
7108 A
1 A
7109 TATTATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.23
31 4 0.13
32 19 0.63
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (32 bp):
AAATGTTTTTTAAAACAAAAACGATAATTAAA
Found at i:7236 original size:16 final size:16
Alignment explanation
Indices: 7204--7280 Score: 59
Period size: 18 Copynumber: 4.6 Consensus size: 16
7194 TGTCACGTCA
7204 ATAAATAATTCAAAAATT
1 ATAAA-AATT-AAAAATT
7222 ATAAAAATTAAAAATT
1 ATAAAAATTAAAAATT
* **
7238 -TAAATAAATCAAAATCAAA
1 AT-AA-AAATTAAAA--ATT
7257 ATAAAAATTAAAAA-T
1 ATAAAAATTAAAAATT
7272 ATAAAAATT
1 ATAAAAATT
7281 TCATAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
15 10 0.20
16 10 0.20
17 12 0.24
18 13 0.27
19 3 0.06
20 1 0.02
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATTAAAAATT
Found at i:7243 original size:33 final size:34
Alignment explanation
Indices: 7204--7280 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 34
7194 TGTCACGTCA
**
7204 ATAAATAATTCAAAA-ATTATAAAAATTAAAAAT
1 ATAAATAATTCAAAACAAAATAAAAATTAAAAAT
* *
7237 TTAAATAAATCAAAATCAAAATAAAAATTAAAAAT
1 ATAAATAATTCAAAA-CAAAATAAAAATTAAAAAT
7272 ATAAA-AATT
1 ATAAATAATT
7281 TCATAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 13 0.36
34 3 0.08
35 20 0.56
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (34 bp):
ATAAATAATTCAAAACAAAATAAAAATTAAAAAT
Found at i:9489 original size:79 final size:79
Alignment explanation
Indices: 9265--9490 Score: 283
Period size: 79 Copynumber: 2.9 Consensus size: 79
9255 CCAACAGTTA
* * * * **
9265 TGGCACCCAGTGCCTAGCGGATAAACCACAATTATGAGCCCAGATCTAGTTGGATT-AACCAACA
1 TGGCACCCAGTGCTTAGCGGATAAACCACAAATATGAGCCCAGCTCTAGTTAG-TTAAACTGACA
* *
9329 ATATTCGTCAAATCT
65 ATGTTCGTCAAATCC
** * * * *
9344 TAACACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAATTGACAA
1 TGGCACCCAGTGCTTAGCGGATAAACCACAAATATGAGCCCAGCTCTAGTTAGTTAAACTGACAA
9409 TGTTCGTCAAATCC
66 TGTTCGTCAAATCC
* * *
9423 TGGCACCCAATGCTTAGCGAATAAACCACAAATATGAGCTCAGCTCTAGTTAGTTAAACTGACAA
1 TGGCACCCAGTGCTTAGCGGATAAACCACAAATATGAGCCCAGCTCTAGTTAGTTAAACTGACAA
9488 TGT
66 TGT
9491 AAGTTATTCA
Statistics
Matches: 123, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
78 2 0.02
79 121 0.98
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (79 bp):
TGGCACCCAGTGCTTAGCGGATAAACCACAAATATGAGCCCAGCTCTAGTTAGTTAAACTGACAA
TGTTCGTCAAATCC
Found at i:10552 original size:41 final size:41
Alignment explanation
Indices: 10495--10590 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
10485 GAATTTTATT
*
10495 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
10536 TTAACAAGAATTCTAGTCATCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
10577 TTGACAAGAATTCT
1 TTAACAAGAATTCT
10591 CTACGAACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.30
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:10602 original size:17 final size:17
Alignment explanation
Indices: 10580--10618 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
10570 CTCCACCTTG
* *
10580 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
10597 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
10614 ACAAG
1 ACAAG
10619 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:14473 original size:17 final size:17
Alignment explanation
Indices: 14451--14489 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
14441 AGATGCAGAA
* *
14451 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
14468 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
14485 CTTGT
1 CTTGT
14490 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:14536 original size:41 final size:41
Alignment explanation
Indices: 14479--14574 Score: 158
Period size: 41 Copynumber: 2.3 Consensus size: 41
14469 TTGTTCGTAG
*
14479 AGAATTCTTGTCAAGGTGGAGATTGTTA-AAGTTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAA-TTGGGTGACT
*
14520 AGAATTCTTGTTAAGGTGGTGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
14561 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
14575 AATAAAATTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 50 0.96
42 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGACT
Found at i:23519 original size:30 final size:32
Alignment explanation
Indices: 23457--23520 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
23447 TTATTTTGAT
* *
23457 TTTTTTTAAAAAAATTGATGATTAACTCTTAA
1 TTTTTTTAAAAAAATTGAAGATTAAATCTTAA
23489 TTTTTTT-AAAAAATT-AAGAGTTAAAT-TTAA
1 TTTTTTTAAAAAAATTGAAGA-TTAAATCTTAA
23519 TT
1 TT
23521 GAATAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.31
31 13 0.45
32 7 0.24
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (32 bp):
TTTTTTTAAAAAAATTGAAGATTAAATCTTAA
Done.