Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000684.1 Kokia drynarioides strain JFW-HI SEQ_111680, 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: 73171
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:1312 original size:6 final size:6
Alignment explanation
Indices: 1282--1315 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1272 TCCATTTCTT
* *
1282 GGAAGG AGAAGG AGAAGG GGAAGG GGAAGG GGAA
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAA
1316 AGAGAGCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:2671 original size:39 final size:38
Alignment explanation
Indices: 2590--2687 Score: 117
Period size: 39 Copynumber: 2.6 Consensus size: 38
2580 ATTTAATTTT
*****
2590 ATAA-TATTTTAATATACGTTTAAAATAATTATTTTTC
1 ATAATTATTTTAATATACGTTTAAAATAATTATGAAAA
*
2627 TTAATTATTTTTAATATACGTTTAAAATAATTATGAAAA
1 ATAATTA-TTTTAATATACGTTTAAAATAATTATGAAAA
*
2666 ATAATTATTTTAATATCCGTTT
1 ATAATTATTTTAATATACGTTT
2688 CATAGCATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 3 0.06
38 16 0.31
39 32 0.63
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (38 bp):
ATAATTATTTTAATATACGTTTAAAATAATTATGAAAA
Found at i:3593 original size:28 final size:28
Alignment explanation
Indices: 3547--3604 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3537 TAAATTTTAA
* *
3547 AAGATTAAATTAAATTTTTATTATTTTT
1 AAGATTAAAGTAAATTTTTATTATTATT
3575 AAGATTAAAGTATAA-TTTTATTATTATT
1 AAGATTAAAGTA-AATTTTTATTATTATT
3603 AA
1 AA
3605 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
AAGATTAAAGTAAATTTTTATTATTATT
Found at i:3854 original size:6 final size:6
Alignment explanation
Indices: 3843--3869 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3833 GTCCCTTTCT
3843 CTCTCA CTCTCA CTCTCA CTCTCA CTC
1 CTCTCA CTCTCA CTCTCA CTCTCA CTC
3870 ATTTGACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCA
Found at i:15660 original size:153 final size:153
Alignment explanation
Indices: 15379--15834 Score: 716
Period size: 153 Copynumber: 3.0 Consensus size: 153
15369 CAAGGTGTCA
* * *
15379 GATGTTGGTTGGGATGCTTTATCTGGATGGAATAAAAATGCTGAGGATGTTGACAAATTTGCAGC
1 GATGTTGGTTGGGATGCTTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
* * * *
15444 AGCTGCGACCAGTTCGGAGAAGCAAAATGAGTGGTCTGGTTGGGGGGCGAGCAAATCTGAATCAC
66 AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGCGAGCAAATCTAAATCAC
* *
15509 AAGTTGTTGTCTCTCCAAAAGTG
131 AAGATGATGTCTCTCCAAAAGTG
*
15532 GATGTTGGTTGGGATGCTTTGTCCGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
1 GATGTTGGTTGGGATGCTTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
*
15597 TGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGCGAGCAAATCTAAATCAC
66 AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGCGAGCAAATCTAAATCAC
*
15662 AAGATGCTGTCTCTCCAAAAGTG
131 AAGATGATGTCTCTCCAAAAGTG
* * *
15685 GATGTTGGTTGGGATGCCTTGTCTGCG-TGGAATAAAAATGCAGAGGATAGTGACAATTTTGCAG
1 GATGTTGGTTGGGATGCTTTGTCTG-GATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAG
* * * **
15749 CAGCTGCATCCAGTTCAAAGAAGCAAAGTGAGTGGTCTGATTGGGGGATGAGCAAATCTAAATCA
65 CAGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGCGAGCAAATCTAAATCA
15814 CAAGATGATGTCTCTCCAAAA
130 CAAGATGATGTCTCTCCAAAA
15835 ACGGATGGAA
Statistics
Matches: 280, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 279 1.00
154 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (153 bp):
GATGTTGGTTGGGATGCTTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGCGAGCAAATCTAAATCAC
AAGATGATGTCTCTCCAAAAGTG
Found at i:16470 original size:36 final size:36
Alignment explanation
Indices: 16387--16596 Score: 204
Period size: 36 Copynumber: 5.8 Consensus size: 36
16377 CTGGAGTAAG
* * ** * **
16387 AATAGTGCTTGGGATCAACAAAAGTCACAGAGAATG
1 AATAGTTCTTGGGACCAACAAAAGTCACCTACAACA
* * * *
16423 AATAATGCTTGGGACCAACAAAAATCACCTGCAACA
1 AATAGTTCTTGGGACCAACAAAAGTCACCTACAACA
** * * * *
16459 AATAGTTCTTGGGACCGGCAAAAATCATCTACGATA
1 AATAGTTCTTGGGACCAACAAAAGTCACCTACAACA
* * *
16495 AATAATTCTTGGGACCAACAAAAGCCACCTACAGCA
1 AATAGTTCTTGGGACCAACAAAAGTCACCTACAACA
* **
16531 AATAGTTCTTGGGACCAAGAAAAGTCACCTACAATG
1 AATAGTTCTTGGGACCAACAAAAGTCACCTACAACA
*
16567 AATAGTTCATGGGACCAACAAAAGTCACCT
1 AATAGTTCTTGGGACCAACAAAAGTCACCT
16597 GAATGTTCTC
Statistics
Matches: 140, Mismatches: 34, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 140 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (36 bp):
AATAGTTCTTGGGACCAACAAAAGTCACCTACAACA
Found at i:16506 original size:72 final size:72
Alignment explanation
Indices: 16387--16597 Score: 226
Period size: 72 Copynumber: 2.9 Consensus size: 72
16377 CTGGAGTAAG
* * * * ** * * * *
16387 AATAGTGCTTGGGATCAACAAAAGTCACAGAGAATGAATAATGCTTGGGACCAACAAAAATCACC
1 AATAGTTCTTGGGACCAAGAAAAATCACCTACAATAAATAATTCTTGGGACCAACAAAAGTCACC
16452 TGCAACA
66 TGCAACA
* * * *
16459 AATAGTTCTTGGGACC-GGCAAAAATCATCTACGATAAATAATTCTTGGGACCAACAAAAGCCAC
1 AATAGTTCTTGGGACCAAG-AAAAATCACCTACAATAAATAATTCTTGGGACCAACAAAAGTCAC
* *
16523 CTACAGCA
65 CTGCAACA
* * * *
16531 AATAGTTCTTGGGACCAAGAAAAGTCACCTACAATGAATAGTTCATGGGACCAACAAAAGTCACC
1 AATAGTTCTTGGGACCAAGAAAAATCACCTACAATAAATAATTCTTGGGACCAACAAAAGTCACC
16596 TG
66 TG
16598 AATGTTCTCA
Statistics
Matches: 112, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
72 111 0.99
73 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.20
Consensus pattern (72 bp):
AATAGTTCTTGGGACCAAGAAAAATCACCTACAATAAATAATTCTTGGGACCAACAAAAGTCACC
TGCAACA
Found at i:18817 original size:42 final size:42
Alignment explanation
Indices: 18695--18901 Score: 249
Period size: 42 Copynumber: 5.0 Consensus size: 42
18685 TTTCAAAAAA
* * * * *
18695 TCTCGAGGGAACCGCGACCGAAGTGTGGCTCCAGA-G--AAT
1 TCTCAAGGGAACCGCGACCAAAGTGTTGCTCAAGATGATAAC
** * * *
18734 TCTCAAGGGCTCCGTGACCGAAGCGTTGCTCAAGATGATAAC
1 TCTCAAGGGAACCGCGACCAAAGTGTTGCTCAAGATGATAAC
* *
18776 TCTCGAGGGAACCGCGATCAAAGTGTTGCTCAAGATGATAAC
1 TCTCAAGGGAACCGCGACCAAAGTGTTGCTCAAGATGATAAC
*
18818 TCTCAAGGGAACCGCAACCAAAGTGTTGCTCAAGATGATAAC
1 TCTCAAGGGAACCGCGACCAAAGTGTTGCTCAAGATGATAAC
* * *
18860 TCTCAAGGGAACCGTGACCAAAGTGTTGCTGAAGACGATAAC
1 TCTCAAGGGAACCGCGACCAAAGTGTTGCTCAAGATGATAAC
18902 GAGGGGGAGG
Statistics
Matches: 143, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
39 28 0.20
40 1 0.01
42 114 0.80
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (42 bp):
TCTCAAGGGAACCGCGACCAAAGTGTTGCTCAAGATGATAAC
Found at i:20080 original size:30 final size:30
Alignment explanation
Indices: 20046--20117 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
20036 TGTTAACAAT
*
20046 AATTTTTATTTTAGTTACCTAACTTTAATA
1 AATTTTTATTTTAGTCACCTAACTTTAATA
* * *
20076 AATTTTCATTTTAGTCACTTAATTTTAATA
1 AATTTTTATTTTAGTCACCTAACTTTAATA
20106 AATTTTTATTTT
1 AATTTTTATTTT
20118 GATCATGCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (30 bp):
AATTTTTATTTTAGTCACCTAACTTTAATA
Found at i:37214 original size:15 final size:15
Alignment explanation
Indices: 37184--37213 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
37174 CACAAATCGC
37184 TAAAAATGAATTTTT
1 TAAAAATGAATTTTT
37199 TAAAAA-GAATTTTT
1 TAAAAATGAATTTTT
37213 T
1 T
37214 TTTTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
TAAAAATGAATTTTT
Found at i:37635 original size:19 final size:20
Alignment explanation
Indices: 37596--37642 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
37586 AACATGCTTG
37596 AAAGTATCGATACCCTAAC-
1 AAAGTATCGATACCCTAACA
** *
37615 AAAGTATCGATACTTTCACA
1 AAAGTATCGATACCCTAACA
37635 AAAGTATC
1 AAAGTATC
37643 AATGCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAGTATCGATACCCTAACA
Found at i:37796 original size:20 final size:20
Alignment explanation
Indices: 37751--37800 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
37741 CTCGTAGCAA
*
37751 GTATCGATACATTCCCTTCT
1 GTATTGATACATTCCCTTCT
* *
37771 GCATTGATACATT-CCTTATT
1 GTATTGATACATTCCCTT-CT
37791 GTATTGATAC
1 GTATTGATAC
37801 TATAGGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (20 bp):
GTATTGATACATTCCCTTCT
Found at i:40874 original size:6 final size:6
Alignment explanation
Indices: 40863--40889 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40853 GAAAAGACTA
40863 CATATC CATATC CATATC CATATC CAT
1 CATATC CATATC CATATC CATATC CAT
40890 CACTTACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATC
Found at i:61275 original size:2 final size:2
Alignment explanation
Indices: 61270--61296 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61260 ATGTTAAATC
61270 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
61297 GAAATGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.