Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007057.1 Kokia drynarioides strain JFW-HI SEQ_121665, 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: 64359
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1783 original size:12 final size:12
Alignment explanation
Indices: 1737--1787 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1727 ACTTTCAACC
*
1737 GCCTGAGCTTGA
1 GCCTGAGCTCGA
* *
1749 GCATGAGCCCGA
1 GCCTGAGCTCGA
*
1761 GCACT-ATCTCGA
1 GC-CTGAGCTCGA
1773 GCCTGAGCTCGA
1 GCCTGAGCTCGA
1785 GCC
1 GCC
1788 CGTGCCGATG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 2 0.07
12 27 0.90
13 1 0.03
ACGTcount: A:0.20, C:0.33, G:0.29, T:0.18
Consensus pattern (12 bp):
GCCTGAGCTCGA
Found at i:2424 original size:21 final size:21
Alignment explanation
Indices: 2381--2424 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2371 TATCGCTTTA
* * *
2381 AATCCAAATCCTTAAAACCCT
1 AATCAAAACCCTTAAAAACCT
*
2402 AATCAAAACCCTTAAAAATCT
1 AATCAAAACCCTTAAAAACCT
2423 AA
1 AA
2425 AACCTTAACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (21 bp):
AATCAAAACCCTTAAAAACCT
Found at i:2559 original size:7 final size:7
Alignment explanation
Indices: 2484--2615 Score: 52
Period size: 7 Copynumber: 17.7 Consensus size: 7
2474 TCTTAAAAAT
*
2484 TTAAAAC
1 TTAAACC
2491 TTAAAACC
1 TT-AAACC
* *
2499 CTAAATC
1 TTAAACC
*
2506 TTACATCC
1 TTA-AACC
*
2514 TAAAACC
1 TTAAACC
2521 TTTAAACC
1 -TTAAACC
2529 ATTAAAACGC
1 -TT-AAAC-C
*
2539 TAAAATCC
1 TTAAA-CC
2547 -TAAACC
1 TTAAACC
2553 TTAAACC
1 TTAAACC
*
2560 TTAAATC
1 TTAAACC
*
2567 ATAAACC
1 TTAAACC
* *
2574 CTAAATCA
1 TTAAA-CC
*
2582 TAAAACC
1 TTAAACC
*
2589 ATAAAACC
1 -TTAAACC
2597 TTAAA-C
1 TTAAACC
2603 TATAAACC
1 T-TAAACC
2611 TTAAA
1 TTAAA
2616 ATCATAACTT
Statistics
Matches: 93, Mismatches: 21, Indels: 22
0.68 0.15 0.16
Matches are distributed among these distances:
6 4 0.04
7 48 0.52
8 34 0.37
9 6 0.06
10 1 0.01
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (7 bp):
TTAAACC
Found at i:2571 original size:14 final size:14
Alignment explanation
Indices: 2554--2643 Score: 63
Period size: 14 Copynumber: 6.8 Consensus size: 14
2544 TCCTAAACCT
2554 TAAACCTTAAATCA
1 TAAACCTTAAATCA
*
2568 TAAACCCTAAATCA
1 TAAACCTTAAATCA
2582 TAAAACC----AT-A
1 T-AAACCTTAAATCA
2592 -AAACCTTAAA-CTA
1 TAAACCTTAAATC-A
2605 TAAACCTTAAAATCA
1 TAAACCTT-AAATCA
2620 T-AA-CTTCAAATCA
1 TAAACCTT-AAATCA
*
2633 TAAACCCTAAA
1 TAAACCTTAAA
2644 CATGTAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
8 5 0.08
10 1 0.02
11 2 0.03
12 1 0.02
13 11 0.18
14 28 0.46
15 12 0.20
16 1 0.02
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAATCA
Found at i:2609 original size:22 final size:22
Alignment explanation
Indices: 2548--2616 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
2538 CTAAAATCCT
*
2548 AAACCTTAAACCT-TAAATCATA
1 AAACCTTAAA-CTATAAACCATA
*
2570 AA-CCCTAAA-TCATAAAACCATA
1 AAACCTTAAACT-AT-AAACCATA
*
2592 AAACCTTAAACTATAAACCTTA
1 AAACCTTAAACTATAAACCATA
2614 AAA
1 AAA
2617 TCATAACTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.03
21 7 0.18
22 21 0.55
23 8 0.21
24 1 0.03
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACCTTAAACTATAAACCATA
Found at i:4950 original size:27 final size:27
Alignment explanation
Indices: 4905--4978 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
4895 GTAGGACTAG
*
4905 TGCCGCCTACCAAGTAGGCACCATTGA
1 TGCCGCCTACCAAGAAGGCACCATTGA
*
4932 TGCCGCCTATCCAA-AAGGCACCATTGG
1 TGCCGCCTA-CCAAGAAGGCACCATTGA
* **
4959 TGCTGCCTACCCCGAAGGCA
1 TGCCGCCTACCAAGAAGGCA
4979 TCACCCGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 34 0.85
28 4 0.10
ACGTcount: A:0.24, C:0.35, G:0.23, T:0.18
Consensus pattern (27 bp):
TGCCGCCTACCAAGAAGGCACCATTGA
Found at i:11845 original size:24 final size:25
Alignment explanation
Indices: 11818--11874 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
11808 CATTGTTTTA
*
11818 ATGTTTACATT-AAAATAGTATTAT
1 ATGTTTACATTAAAAAAAGTATTAT
*
11842 ATGTTTATATTAAAAAAAAGTATTAT
1 ATGTTTACATT-AAAAAAAGTATTAT
*
11868 ATATTTA
1 ATGTTTA
11875 GTATATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.36
26 18 0.64
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (25 bp):
ATGTTTACATTAAAAAAAGTATTAT
Found at i:31186 original size:57 final size:57
Alignment explanation
Indices: 31118--31233 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
31108 TTTACGTCCT
* *
31118 GTATCACGTGGCCCGGCTCAAGGAGTATCGGAGAAAACGAGCGGGATTTGGGCCGGC
1 GTATCACGTGGCCCGGCTCAAGGAGTATCAGAGAAAACGAGCGGGATTAGGGCCGGC
* *
31175 GTATCACGTGGCCCGGCTCAAGGATTATCAGAGAAAACGAGCGGGATTAGGGCTGGC
1 GTATCACGTGGCCCGGCTCAAGGAGTATCAGAGAAAACGAGCGGGATTAGGGCCGGC
31232 GT
1 GT
31234 CCCCGAGAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.24, C:0.22, G:0.37, T:0.17
Consensus pattern (57 bp):
GTATCACGTGGCCCGGCTCAAGGAGTATCAGAGAAAACGAGCGGGATTAGGGCCGGC
Found at i:39994 original size:51 final size:51
Alignment explanation
Indices: 39935--40046 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
39925 ATGCTGATCG
* * *
39935 AATGTGTAAATTTTTTAAGTTAAATTTGATAAATCAGGACCAACTTGACAA
1 AATGTGTAAATGTTGTAAGTTAAATTTGATAAATCAAGACCAACTTGACAA
** * * * *
39986 AATGTGTAAATGTTGTGGGTTAAATTTGTTAAATTAAGACCAAGTTGATAA
1 AATGTGTAAATGTTGTAAGTTAAATTTGATAAATCAAGACCAACTTGACAA
40037 AATGTGTAAA
1 AATGTGTAAA
40047 CTTTAAGAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (51 bp):
AATGTGTAAATGTTGTAAGTTAAATTTGATAAATCAAGACCAACTTGACAA
Found at i:44427 original size:2 final size:2
Alignment explanation
Indices: 44420--44444 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44410 CTATGGCATC
44420 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
44445 ATATTTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:56324 original size:13 final size:14
Alignment explanation
Indices: 56306--56335 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56296 GGAGAATGAC
56306 TTTAAAA-GTATTT
1 TTTAAAAGGTATTT
56319 TTTAAAAGGTATTT
1 TTTAAAAGGTATTT
56333 TTT
1 TTT
56336 TTTCACATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (14 bp):
TTTAAAAGGTATTT
Found at i:57915 original size:6 final size:6
Alignment explanation
Indices: 57904--57933 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
57894 TAAACAGCAT
57904 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
57934 TATATCGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (6 bp):
CTTTTG
Found at i:63843 original size:6 final size:6
Alignment explanation
Indices: 63832--63861 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
63822 GGCTCATCCT
63832 CTATTC CTATTC CTATTC CTATTC CTATTC
1 CTATTC CTATTC CTATTC CTATTC CTATTC
63862 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
CTATTC
Done.