Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005495.1 Kokia drynarioides strain JFW-HI SEQ_119558, 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: 43888
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:6281 original size:21 final size:20
Alignment explanation
Indices: 6238--6282 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6228 CTCGATTTTC
* *
6238 GTTTGTAATGATTTGTGGAT
1 GTTTGGAATGATTTATGGAT
*
6258 GTTTGGAATGATTTAATTGAT
1 GTTTGGAATGATTT-ATGGAT
6279 GTTT
1 GTTT
6283 ATAGCTTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (20 bp):
GTTTGGAATGATTTATGGAT
Found at i:7814 original size:15 final size:16
Alignment explanation
Indices: 7783--7816 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7773 TTGATATGTG
7783 ATTTTTTAAAATATTT
1 ATTTTTTAAAATATTT
*
7799 ATTTTTTAATAT-TTT
1 ATTTTTTAAAATATTT
7814 ATT
1 ATT
7817 ATATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTAAAATATTT
Found at i:16679 original size:20 final size:22
Alignment explanation
Indices: 16634--16679 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
16624 AATTTTTTAA
16634 AATTAAAAATTATAAAAATATT
1 AATTAAAAATTATAAAAATATT
*
16656 --TTAAAAATT-T-TAAATATT
1 AATTAAAAATTATAAAAATATT
16674 AATTAA
1 AATTAA
16680 TTACTAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTAAAAATTATAAAAATATT
Found at i:20070 original size:31 final size:29
Alignment explanation
Indices: 20015--20074 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
20005 ATATTTTAAA
* * *
20015 CGGGCTTAATTTTTTGTTCTAACCCATTTT
1 CGGGATTAATTTTTTGTCCAAACCC-TTTT
20045 CGGGATTAATATTTTTGTCCAAACCCTTTT
1 CGGGATTAAT-TTTTTGTCCAAACCCTTTT
20075 AAATTTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (29 bp):
CGGGATTAATTTTTTGTCCAAACCCTTTT
Found at i:32333 original size:3 final size:3
Alignment explanation
Indices: 32325--32361 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
32315 AAGAACGCTT
32325 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
32362 ATATAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:35506 original size:44 final size:43
Alignment explanation
Indices: 35456--35663 Score: 204
Period size: 45 Copynumber: 4.7 Consensus size: 43
35446 GGAATGAATG
* *
35456 AGACCATAGTTGAAAGATACTATGGCATTACATT-GACTTAAGTA
1 AGACCATAGTTGAAAGATACTATGGCATCA-ATTGGA-ATAAGTA
* *
35500 AGACCATAGTTGAAAGATACTATGGCATTAACTTGAGAATATGTA
1 AGACCATAGTTGAAAGATACTATGGCATCAA-TTG-GAATAAGTA
* * *
35545 AGACCGTAGTTGAAAGATACTATGGCATCAAATTCG-ATATGTATA
1 AGACCATAGTTGAAAGATACTATGGCATC-AATTGGAATAAG--TA
* * * *
35590 AGACCTTAGTTGAAAGACACTATGGCATCATATTGGGAAAAATTA
1 AGACCATAGTTGAAAGATACTATGGCATCA-ATT-GGAATAAGTA
* *
35635 AGACTATAGTTGAAAGATATTATGGCATC
1 AGACCATAGTTGAAAGATACTATGGCATC
35664 TTTCCGGAGT
Statistics
Matches: 140, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.04
44 34 0.24
45 93 0.66
46 5 0.04
47 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (43 bp):
AGACCATAGTTGAAAGATACTATGGCATCAATTGGAATAAGTA
Found at i:35679 original size:90 final size:89
Alignment explanation
Indices: 35456--35696 Score: 244
Period size: 90 Copynumber: 2.7 Consensus size: 89
35446 GGAATGAATG
* * *
35456 AGACCATAGTTGAAAGATACTATGGCATTACATT-G--ACTTAAGTAAGACCATAGTTGAAAGAT
1 AGACCATAGTTGAAAGATACTATGGCATCA-ATTCGATACGT-A-TAAGACCATAGTTGAAAGAC
* *
35518 ACTATGGCATTAACTTGAGAATATGTA
63 ACTATGGCATCAACTTGAGAAAATGTA
* * *
35545 AGACCGTAGTTGAAAGATACTATGGCATCAAATTCGATATGTATAAGACCTTAGTTGAAAGACAC
1 AGACCATAGTTGAAAGATACTATGGCATC-AATTCGATACGTATAAGACCATAGTTGAAAGACAC
*
35610 TATGGCATCATA-TTGGGAAAAAT-TA
65 TATGGCATCA-ACTTGAG-AAAATGTA
* * *
35635 AGACTATAGTTGAAAGATATTATGGCATC-TTTCCGGAGT-CGTATAAGACCATAGTTGAAAGA
1 AGACCATAGTTGAAAGATACTATGGCATCAATT-C-GA-TACGTATAAGACCATAGTTGAAAGA
35697 TACCCTAATA
Statistics
Matches: 128, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
88 2 0.02
89 31 0.24
90 86 0.67
91 7 0.05
92 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (89 bp):
AGACCATAGTTGAAAGATACTATGGCATCAATTCGATACGTATAAGACCATAGTTGAAAGACACT
ATGGCATCAACTTGAGAAAATGTA
Found at i:36491 original size:17 final size:17
Alignment explanation
Indices: 36461--36505 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
36451 TATGACACGA
36461 GCTATCACACGGTCATGT
1 GCTA-CACACGGTCATGT
* *
36479 GCTACACATGGTCGTGT
1 GCTACACACGGTCATGT
*
36496 GCTGCACACG
1 GCTACACACG
36506 ATCTCCCCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (17 bp):
GCTACACACGGTCATGT
Found at i:37398 original size:8 final size:8
Alignment explanation
Indices: 37385--37409 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
37375 AATTCCAAGC
37385 CAATTTCA
1 CAATTTCA
37393 CAATTTCA
1 CAATTTCA
37401 CAATTTCA
1 CAATTTCA
37409 C
1 C
37410 CAAGTTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (8 bp):
CAATTTCA
Found at i:38414 original size:19 final size:19
Alignment explanation
Indices: 38369--38435 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
38359 CTTTTATATT
* *
38369 TTAATTAAATTAAGTAATC
1 TTAATTAAATTAATTAAAC
* **
38388 ATGCTTAAATTAATTAAAC
1 TTAATTAAATTAATTAAAC
38407 TTAATT-AATTAAAACTTAAAC
1 TTAATTAAATT--AA-TTAAAC
38428 TTAATTAA
1 TTAATTAA
38436 CTAATTTAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
18 4 0.11
19 17 0.47
20 2 0.06
21 12 0.33
22 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (19 bp):
TTAATTAAATTAATTAAAC
Found at i:38437 original size:15 final size:15
Alignment explanation
Indices: 38391--38435 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
38381 AGTAATCATG
38391 CTTAAATTAATTAAA
1 CTTAAATTAATTAAA
38406 CTT-AATTAATTAAAA
1 CTTAAATTAATT-AAA
38421 CTTAAACTTAATTAA
1 CTTAAA-TTAATTAA
38436 CTAATTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.30
15 9 0.33
16 4 0.15
17 6 0.22
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTAAATTAATTAAA
Done.