Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013283.1 Kokia drynarioides strain JFW-HI SEQ_128304, 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: 41302
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 524 characters in sequence are not A, C, G, or T
Found at i:3355 original size:22 final size:23
Alignment explanation
Indices: 3321--3383 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
3311 ACACTAGCGC
*
3321 GCTCTCTGATTAGCACTGTGT-GT
1 GCTCTCTGATTAGCAC-GTCTCGT
*
3344 GCTCTCT-TTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACGTCTCGT
3366 GCTCTCTGTTATTAGCAC
1 GCTCTCTG--ATTAGCAC
3384 TTGNNNNNNN
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.09
22 16 0.48
23 7 0.21
25 7 0.21
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACGTCTCGT
Found at i:10025 original size:51 final size:51
Alignment explanation
Indices: 9919--10147 Score: 250
Period size: 51 Copynumber: 4.5 Consensus size: 51
9909 TTTCATTTAA
* ** * * *
9919 TACTCACGATGACA-TATAGTCATCGAACCTCTTGTTCTGTATAGAAATTCA--
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCGTAAAG-GATTCATT
* * * *
9970 TACTCACGATGACA-TTGAGTCATCGGGCCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
10021 TACTCATGATGACACTTAGTCATCGGACTTTTAATCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
10072 TACTCACAATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
*
10123 TACTCAAGATGACACTTAGTCATCG
1 TACTCACGATGACACTTAGTCATCG
10148 AACCCTTTCA
Statistics
Matches: 150, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
49 5 0.03
50 7 0.05
51 136 0.91
52 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:15154 original size:15 final size:13
Alignment explanation
Indices: 15134--15197 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 13
15124 GAGGCAGAGG
15134 AAGAAGGAGGAAAAA
1 AAGAAGGA--AAAAA
*
15149 AAGAA-GAAAAAG
1 AAGAAGGAAAAAA
15161 AAG-AGGAAAAAAA
1 AAGAAGG-AAAAAA
*
15174 AGAGAAGGAAGAAA
1 A-AGAAGGAAAAAA
15188 AAGAA-GAAAA
1 AAGAAGGAAAA
15198 TATTACCCCG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
11 1 0.02
12 12 0.29
13 10 0.24
14 10 0.24
15 8 0.20
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAGAAGGAAAAAA
Found at i:15160 original size:9 final size:9
Alignment explanation
Indices: 15146--15197 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
15136 GAAGGAGGAA
15146 AAAAAGAAG
1 AAAAAGAAG
15155 AAAAAGAAGAGG
1 AAAAAG-A-A-G
*
15167 AAAAAAAAG
1 AAAAAGAAG
* *
15176 AGAAGGAAG
1 AAAAAGAAG
15185 AAAAAGAAG
1 AAAAAGAAG
15194 AAAA
1 AAAA
15198 TATTACCCCG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 24 0.71
10 2 0.06
11 2 0.06
12 6 0.18
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:15185 original size:24 final size:25
Alignment explanation
Indices: 15131--15186 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
15121 ATTGAGGCAG
15131 AGGAAGAAGGAGGAAAAAAAGAAGA
1 AGGAAGAAGGAGGAAAAAAAGAAGA
*
15156 A-AAAGAA-GAGGAAAAAAA-AGAGA
1 AGGAAGAAGGAGGAAAAAAAGA-AGA
15179 AGGAAGAA
1 AGGAAGAA
15187 AAAGAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 15 0.56
24 10 0.37
25 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
AGGAAGAAGGAGGAAAAAAAGAAGA
Found at i:15622 original size:17 final size:18
Alignment explanation
Indices: 15587--15625 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
15577 TGCATGCATT
15587 TTTTATATTGTCTCTGCA
1 TTTTATATTGTCTCTGCA
15605 TTTTAT-TTGT-TCTAGCA
1 TTTTATATTGTCTCT-GCA
15622 TTTT
1 TTTT
15626 GCATTGTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 11 0.55
18 6 0.30
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTATATTGTCTCTGCA
Found at i:19009 original size:23 final size:23
Alignment explanation
Indices: 18983--19026 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
18973 CTACTATTTG
18983 TGCTACTATG-TGTTTACTGTTGC
1 TGCTACT-TGCTGTTTACTGTTGC
*
19006 TGCTACTTGCTGTTTTCTGTT
1 TGCTACTTGCTGTTTACTGTT
19027 TGTTTTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.09, C:0.18, G:0.20, T:0.52
Consensus pattern (23 bp):
TGCTACTTGCTGTTTACTGTTGC
Found at i:19382 original size:43 final size:43
Alignment explanation
Indices: 19321--19408 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
19311 GTTAGTTGCC
19321 AAAACTTATTTTTGACACTTGATTGTTTTTCCTAGTCTTTCTA
1 AAAACTTATTTTTGACACTTGATTGTTTTTCCTAGTCTTTCTA
19364 AAAACTTATTTTTGACACTTGATTGTTTTTCCTAGTCTTTCTA
1 AAAACTTATTTTTGACACTTGATTGTTTTTCCTAGTCTTTCTA
19407 AA
1 AA
19409 TTGTGTCCGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (43 bp):
AAAACTTATTTTTGACACTTGATTGTTTTTCCTAGTCTTTCTA
Found at i:19746 original size:98 final size:98
Alignment explanation
Indices: 19572--19765 Score: 246
Period size: 98 Copynumber: 2.0 Consensus size: 98
19562 GGAATAATAA
* * * * *
19572 ATTAGGAGTGTGTTGGACCGAGTAACCGAGATGGAGTGCTTGGGTTTTCATTTCATTTCGTGTCA
1 ATTAGGAGTGTGTTGGACCGAGTAACCAAGACGGAGTGCCTGGGTTGTCATTTCATTTCGTATCA
*
19637 AAAGGGATAATACATTCTTAAATAAAAAAAATG
66 AAAGGGATAATACATTCTTAAAGAAAAAAAATG
* * *
19670 ATTAGGAGTGTGTTGGGCTGAGTAACCAAGACGGAGTGCCTGGGTTGTGATTTCATTTC-TCATC
1 ATTAGGAGTGTGTTGGACCGAGTAACCAAGACGGAGTGCCTGGGTTGTCATTTCATTTCGT-ATC
* ** * *
19734 AGAAGGTCTAATATATTCTTAAAGAAATAAAA
65 AAAAGGGATAATACATTCTTAAAGAAAAAAAA
19766 GAGAGGAAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 1 0.01
98 80 0.99
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (98 bp):
ATTAGGAGTGTGTTGGACCGAGTAACCAAGACGGAGTGCCTGGGTTGTCATTTCATTTCGTATCA
AAAGGGATAATACATTCTTAAAGAAAAAAAATG
Found at i:27444 original size:24 final size:24
Alignment explanation
Indices: 27383--27445 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
27373 TAGACTAATA
* *
27383 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * *
27407 AGAGTTTAATTGAAACAATTAAAT
1 AGAGTTTAACTGAAACAAATAAAC
27431 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
27446 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:29549 original size:43 final size:43
Alignment explanation
Indices: 29483--29604 Score: 165
Period size: 43 Copynumber: 2.8 Consensus size: 43
29473 TCAATCAATA
*
29483 ACATA-TTATCAATATTAGAAAACAGTGTTCCATTCATTCGATC
1 ACATACTT-TCAATATTAGGAAACAGTGTTCCATTCATTCGATC
* *
29526 ACATACTTTCAATATTAGGAAACAATGTTCCACTCATTCGATC
1 ACATACTTTCAATATTAGGAAACAGTGTTCCATTCATTCGATC
* * * *
29569 ACATACTTCCAATATTTGGAAACAGTGCTCCTTTCA
1 ACATACTTTCAATATTAGGAAACAGTGTTCCATTCA
29605 ATGTCATTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 67 0.97
44 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (43 bp):
ACATACTTTCAATATTAGGAAACAGTGTTCCATTCATTCGATC
Found at i:38564 original size:52 final size:52
Alignment explanation
Indices: 38476--38710 Score: 375
Period size: 52 Copynumber: 4.5 Consensus size: 52
38466 ATTTCATTTC
* *
38476 ATTCATATACTCACGATGACACATAGCCATCAGACCTCATAATCCGTACAA-G
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA-AAGG
* *
38528 ATTCATATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
*
38580 ATTCATATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
* *
38632 ATTCATATACTAACGATGACACATAGTCATCGGACTTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
*
38684 ATTCATATACTCATGATGACACA-AGTC
1 ATTCATATACTCACGATGACACATAGTC
38711 TTAACCATAA
Statistics
Matches: 170, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
51 6 0.04
52 164 0.96
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGG
Done.