Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006945.1 Kokia drynarioides strain JFW-HI SEQ_121550, 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: 44320
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:51 original size:21 final size:22
Alignment explanation
Indices: 16--86 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 22
6 ACCAGCACCG
*
16 CCTCCAACACC-ACCTCCTATA
1 CCTCCACCACCTACCTCCTATA
* **
37 CCTCCACCA-GTACCTCCTCCA
1 CCTCCACCACCTACCTCCTATA
* *
58 GCTCCACCACCTA-CTCCTATG
1 CCTCCACCACCTACCTCCTATA
79 CCTCCACC
1 CCTCCACC
87 TTTTCCACCA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 36 0.95
22 2 0.05
ACGTcount: A:0.21, C:0.55, G:0.04, T:0.20
Consensus pattern (22 bp):
CCTCCACCACCTACCTCCTATA
Found at i:190 original size:24 final size:23
Alignment explanation
Indices: 163--244 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 23
153 TGCACCGGCT
163 CCACCTCCAAAGCCTCCACCTAAA
1 CCACCTCCAAAGCCTCCACC-AAA
* ** * *
187 CCACCACCATGGCCACCACCAACC
1 CCACCTCCAAAGCCTCCACCAA-A
* *
211 CCTCCTCCAGCA-CCTCCACCGAAA
1 CCACCTCCA-AAGCCTCCACC-AAA
235 CCACCTCCAA
1 CCACCTCCAA
245 GGGTTTCCTT
Statistics
Matches: 42, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.29, C:0.55, G:0.06, T:0.10
Consensus pattern (23 bp):
CCACCTCCAAAGCCTCCACCAAA
Found at i:10158 original size:6 final size:6
Alignment explanation
Indices: 10149--10219 Score: 112
Period size: 6 Copynumber: 12.3 Consensus size: 6
10139 GCAACAGCAA
10149 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
*
10197 AAAGGG AG-GGG AG-GGG AG-GGG AG
1 AGAGGG AGAGGG AGAGGG AGAGGG AG
10220 GATTTTTTTA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
5 15 0.24
6 48 0.76
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:19462 original size:3 final size:3
Alignment explanation
Indices: 19454--19479 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19444 GGACTGAGCA
19454 TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TG
19480 TTGTTGGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.35, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:20382 original size:18 final size:18
Alignment explanation
Indices: 20359--20401 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20349 TTTTCAATTG
20359 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
20377 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
20395 TAATTAA
1 TAATTAA
20402 AATTTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:23110 original size:26 final size:26
Alignment explanation
Indices: 23079--23138 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
23069 TTTACCATAA
23079 TAAAATTTTGAA-GATTTTATCCC-TGG
1 TAAAATTTT-AACGATTTT-TCCCTTGG
23105 TAAAATTTTAACGATTTTTCCCTTGG
1 TAAAATTTTAACGATTTTTCCCTTGG
23131 TAAAATTT
1 TAAAATTT
23139 CAAAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (26 bp):
TAAAATTTTAACGATTTTTCCCTTGG
Found at i:27654 original size:36 final size:36
Alignment explanation
Indices: 27612--27715 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
27602 TAGTAACAAG
*
27612 CATGACCTTTAGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
27648 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
* *
27684 TATGACCTTTGGGTCAACAGGGAGTAAAACGA
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGA
27716 ATAACAAACG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
Found at i:28400 original size:21 final size:21
Alignment explanation
Indices: 28376--28429 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
28366 AGAGTTTTTG
* *
28376 GTGTCGGTAGAAGTAAGACTT
1 GTGTCGGTAGAACTAACACTT
*
28397 GTGTCGGTAGAACTGACACTT
1 GTGTCGGTAGAACTAACACTT
*
28418 GTATCGGTAGAA
1 GTGTCGGTAGAA
28430 AATTATACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (21 bp):
GTGTCGGTAGAACTAACACTT
Found at i:30498 original size:23 final size:22
Alignment explanation
Indices: 30471--30517 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
30461 TTTCAAGGAA
*
30471 TTTTATTTTTAAGTTTTGAGGGT
1 TTTTATTTTTAAGTTGT-AGGGT
*
30494 TTTTATTTTTAGGTTGTAGGGT
1 TTTTATTTTTAAGTTGTAGGGT
30516 TT
1 TT
30518 AGTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (22 bp):
TTTTATTTTTAAGTTGTAGGGT
Found at i:30858 original size:3 final size:3
Alignment explanation
Indices: 30850--30874 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30840 AAAGTAGAGC
30850 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
30875 TCATTGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:32994 original size:36 final size:36
Alignment explanation
Indices: 32947--33072 Score: 189
Period size: 36 Copynumber: 3.5 Consensus size: 36
32937 AGTAACAGGC
*
32947 ATGACCTTTGGGTCAACAGGGAGAAAAATGAGCATA
1 ATGACCTTTAGGTCAACAGGGAGAAAAATGAGCATA
* *
32983 ATGACCTTTGGGTCAATAGGGAGAAAAATGAGCATA
1 ATGACCTTTAGGTCAACAGGGAGAAAAATGAGCATA
* * *
33019 ATGACATTTAGGTCAACAGAGACAAAAATGAGCATA
1 ATGACCTTTAGGTCAACAGGGAGAAAAATGAGCATA
*
33055 ATAACCTTTAGGTCAACA
1 ATGACCTTTAGGTCAACA
33073 AAGAGGAAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (36 bp):
ATGACCTTTAGGTCAACAGGGAGAAAAATGAGCATA
Found at i:33779 original size:116 final size:116
Alignment explanation
Indices: 33575--33838 Score: 395
Period size: 116 Copynumber: 2.3 Consensus size: 116
33565 GACAGAACTC
*
33575 ATGCTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTATTTCGTTA
1 ATGCTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTATTTCGGTA
* * *
33640 GTTGTATAACAAGTATCGATAGTTCTATATATTGAGGTATCAGTAGTTTAA
66 ATTGTATAACAAGTATCGATAGTTCTATACATTGAGGTATCAGTAGCTTAA
* * *
33691 ATGCTTGTATTGGTAGTAA-TACAGGGTAGGAGAGAGGTTGTTCTTTGACTTGAGTTATTTGGGT
1 ATGCTTGTATCGGTAG-AAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTATTTCGGT
* * * *
33755 AATTGTATAACAGGTATCGGTAGTTCTGTACATTGAGGTATCGGTAGCTTAA
65 AATTGTATAACAAGTATCGATAGTTCTATACATTGAGGTATCAGTAGCTTAA
*
33807 ATACTTGTATCGGTAGAAGTTACAGGGTAGGA
1 ATGCTTGTATCGGTAGAAG-TACAGGGTAGGA
33839 CTTCTTAGCT
Statistics
Matches: 132, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
115 2 0.02
116 116 0.88
117 14 0.11
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (116 bp):
ATGCTTGTATCGGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTCTGACTTGAGTTATTTCGGTA
ATTGTATAACAAGTATCGATAGTTCTATACATTGAGGTATCAGTAGCTTAA
Found at i:41281 original size:39 final size:39
Alignment explanation
Indices: 41227--41303 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
41217 CGAGCTTCAT
41227 ATAGTTGATTCATCAGCAAAAAATTACAAATCAAAGTAA
1 ATAGTTGATTCATCAGCAAAAAATTACAAATCAAAGTAA
41266 ATAGTTGATTCATCAGCAAAAAATTACAAATCAAAGTA
1 ATAGTTGATTCATCAGCAAAAAATTACAAATCAAAGTA
41304 TCTTAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (39 bp):
ATAGTTGATTCATCAGCAAAAAATTACAAATCAAAGTAA
Found at i:41765 original size:18 final size:18
Alignment explanation
Indices: 41710--41765 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
41700 ATAATCTTCA
41710 TTTTTCTTCTTCTTCTTTTTC
1 TTTTTCTT-TT-TT-TTTTTC
*
41731 TTTTTCTTTTTCTTTTTC
1 TTTTTCTTTTTTTTTTTC
41749 TTTTTCTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTT
41766 TGTTATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 22 0.67
19 1 0.03
20 2 0.06
21 8 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTTTC
Found at i:41766 original size:6 final size:6
Alignment explanation
Indices: 41716--41764 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
41706 TTCATTTTTC
*
41716 TTCTTC TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT-TTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
41763 TT
1 TT
41765 TTGTTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Done.