Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007477.1 Kokia drynarioides strain JFW-HI SEQ_122100, 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: 77331
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1433 original size:25 final size:25
Alignment explanation
Indices: 1405--1454 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1395 ATGTTCCCGA
1405 ACGTTTTATATAATTATATTTCAAT
1 ACGTTTTATATAATTATATTTCAAT
*
1430 ACGTTTTATGTAATTATATTTCAAT
1 ACGTTTTATATAATTATATTTCAAT
1455 CTGGTGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (25 bp):
ACGTTTTATATAATTATATTTCAAT
Found at i:19680 original size:80 final size:80
Alignment explanation
Indices: 19542--19724 Score: 296
Period size: 80 Copynumber: 2.3 Consensus size: 80
19532 ATTGGGAAGG
* * * *
19542 GATAGATCAAAT-TTGATGTGGAATCACAATTTTTTACAATCTCTTCTATCCTTGTGATAGCTTA
1 GATAGATCAAATCTT-ACGTGGAATCACAATTTTATACAATCTCTTATATCCTTATGATAGCTTA
19606 GTCATCAGTTCAAAAT
65 GTCATCAGTTCAAAAT
19622 GATAGATCAAATCTTACGTGGAATCACAATTTTATACAATCTCTTATATCCTTATGATAGCTTAG
1 GATAGATCAAATCTTACGTGGAATCACAATTTTATACAATCTCTTATATCCTTATGATAGCTTAG
19687 TCATCAGTTCAAAAT
66 TCATCAGTTCAAAAT
* *
19702 AATAGATCAAATCTGACGTGGAA
1 GATAGATCAAATCTTACGTGGAA
19725 CATACTTGAA
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 94 0.98
81 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (80 bp):
GATAGATCAAATCTTACGTGGAATCACAATTTTATACAATCTCTTATATCCTTATGATAGCTTAG
TCATCAGTTCAAAAT
Found at i:21857 original size:27 final size:27
Alignment explanation
Indices: 21827--21878 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
21817 AAAACAATGG
* *
21827 CATGAAACATGTTGAAAGACAGTAACC
1 CATGAAACATGCTCAAAGACAGTAACC
21854 CATGAAACATGCTCAAAGACAGTAA
1 CATGAAACATGCTCAAAGACAGTAA
21879 GTAAAGGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.17
Consensus pattern (27 bp):
CATGAAACATGCTCAAAGACAGTAACC
Found at i:32553 original size:6 final size:6
Alignment explanation
Indices: 32542--32593 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
32532 TTTTTTTCAT
* * * *
32542 ACATAC ACAT-- ACATAC ACATAC ACACAC ACACAC ACACAC ACACAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
32588 ACATAC
1 ACATAC
32594 GTACATACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 4 0.10
6 38 0.90
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (6 bp):
ACATAC
Found at i:32563 original size:16 final size:16
Alignment explanation
Indices: 32542--32610 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
32532 TTTTTTTCAT
*
32542 ACATACACATACATAC
1 ACATACACATACACAC
32558 ACATACAC--ACACAC
1 ACATACACATACACAC
* *
32572 ACACACACACACACAC
1 ACATACACATACACAC
32588 ACATACGTACATACA-A-
1 ACATAC--ACATACACAC
32604 ACATACA
1 ACATACA
32611 TACATTGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 13 0.29
16 25 0.56
17 1 0.02
18 6 0.13
ACGTcount: A:0.51, C:0.36, G:0.01, T:0.12
Consensus pattern (16 bp):
ACATACACATACACAC
Found at i:36178 original size:88 final size:88
Alignment explanation
Indices: 36069--36246 Score: 266
Period size: 88 Copynumber: 2.0 Consensus size: 88
36059 TGAAATTACG
* * *
36069 ATCGCAGATATTGACAATAATCACATAAGACCCACCCAGACGAACAAATGATTGATGAGTAAACA
1 ATCGCAGATATTGACAATAATCAAATAAGACCCACCCAAACGAACAAATGACTGATGAGTAAACA
36134 TCATTAATGTTCCGGTGAATCCA
66 TCATTAATGTTCCGGTGAATCCA
* ** * * **
36157 ATCGTAGATATTGATGATAATCAAATAAGGCCCACCCAAACGAGCTGATGACTGATGAGTAAACA
1 ATCGCAGATATTGACAATAATCAAATAAGACCCACCCAAACGAACAAATGACTGATGAGTAAACA
36222 TCATTAATGTTCCGGTGAATCCA
66 TCATTAATGTTCCGGTGAATCCA
36245 AT
1 AT
36247 AAAATGATAG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (88 bp):
ATCGCAGATATTGACAATAATCAAATAAGACCCACCCAAACGAACAAATGACTGATGAGTAAACA
TCATTAATGTTCCGGTGAATCCA
Found at i:37525 original size:22 final size:22
Alignment explanation
Indices: 37498--37539 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
37488 AAGTTCACCC
37498 ATATTATTATT-TTTAAATATCT
1 ATATTA-TATTATTTAAATATCT
*
37520 ATATTATATTATTTTAATAT
1 ATATTATATTATTTAAATAT
37540 TTAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTATATTATTTAAATATCT
Found at i:42105 original size:4 final size:4
Alignment explanation
Indices: 42096--42124 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
42086 ATTCAATTTA
42096 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
42125 GTGTGTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:45796 original size:34 final size:35
Alignment explanation
Indices: 45738--45806 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
45728 GTCAAAATTG
*
45738 AACTTGAATATTTTAAAAAAATTAAGTCTTTATTT
1 AACTTGAATATTTTAAAAAAATTAAGTCATTATTT
45773 AACTTGAATATTTT-AAAAAATTAAGTCATTATTT
1 AACTTGAATATTTTAAAAAAATTAAGTCATTATTT
45807 GGCTTAGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.58
35 14 0.42
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
AACTTGAATATTTTAAAAAAATTAAGTCATTATTT
Found at i:47476 original size:6 final size:6
Alignment explanation
Indices: 47465--47491 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47455 GAATCGATTC
47465 ATTTTA ATTTTA ATTTTA ATTTTA ATT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATT
47492 ATAGTAATTA
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:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:58385 original size:2 final size:2
Alignment explanation
Indices: 58378--58404 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58368 TGAGAATGAG
58378 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
58405 CATTTTTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.