Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011273.1 Kokia drynarioides strain JFW-HI SEQ_126252, 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: 71905
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:271 original size:9 final size:9
Alignment explanation
Indices: 246--279 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
236 GTGAACAAAA
246 AAAATAA-T
1 AAAATAATT
254 AAAAT-ATT
1 AAAATAATT
262 AAAATAATT
1 AAAATAATT
271 AAAATAATT
1 AAAATAATT
280 GTTATAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 1 0.04
8 11 0.46
9 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATAATT
Found at i:618 original size:18 final size:17
Alignment explanation
Indices: 597--642 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
587 ATAAAAAATT
597 ATTTTTATTAGTATTTTA
1 ATTTTTATTA-TATTTTA
*
615 ATTTTAATATATATTTTA
1 ATTTTTAT-TATATTTTA
633 ATATTTTATT
1 AT-TTTTATT
643 TTCTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTATTATATTTTA
Found at i:1312 original size:6 final size:6
Alignment explanation
Indices: 1303--1336 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1293 AAACAGAAAC
*
1303 AGAGGG AGAGGG AGAGGG AGAGGG AGAGCG AGAG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAG
1337 ACAGCGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.62, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:6827 original size:25 final size:23
Alignment explanation
Indices: 6776--6820 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6766 AGTGCTGGGT
*
6776 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTACTA
*
6799 AACAGAGAGTACACAAAGTACT
1 AACAGAGAGCACACAAAGTACT
6821 GAGAACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTACTA
Found at i:6856 original size:23 final size:23
Alignment explanation
Indices: 6825--6964 Score: 133
Period size: 23 Copynumber: 6.0 Consensus size: 23
6815 AGTACTGAGA
* **
6825 ACACAAAGTGCTAATTAGAGAGC
1 ACACGAAGTGCTAAACAGAGAGC
*
6848 ACACGAAGTGCTAATAACAAAGAGC
1 ACACGAAGTGCT-A-AACAGAGAGC
*
6873 ACGA-GACGTGCTAAACAGAGAGC
1 AC-ACGAAGTGCTAAACAGAGAGC
*
6896 ACAC-ACAGTGCTAAACAGAGGGC
1 ACACGA-AGTGCTAAACAGAGAGC
* *
6919 ACAAGCAGTGCTAAACAGAGAGC
1 ACACGAAGTGCTAAACAGAGAGC
*
6942 ACAC-ACAGTGCTAATCAGAGAGC
1 ACACGA-AGTGCTAAACAGAGAGC
6965 GCGCAAGTGT
Statistics
Matches: 96, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.02
23 75 0.78
24 2 0.02
25 16 0.17
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
ACACGAAGTGCTAAACAGAGAGC
Found at i:6944 original size:46 final size:45
Alignment explanation
Indices: 6776--6964 Score: 176
Period size: 46 Copynumber: 4.2 Consensus size: 45
6766 AGTGCTGGGT
* * *
6776 AACAGAGAGCACACAAAGTGCTAAACAGAGAGTACACA-A-AG-T-
1 AACAGAGAGCACA-AGAGTGCTAAACAGAGAGCACACACAGTGCTA
* * **
6818 -ACTGAGAACACAA-AGTGCTAATTAGAGAGCACACGA-AGTGCTAA
1 AACAGAGAGCACAAGAGTGCTAAACAGAGAGCACAC-ACAGTGCT-A
* *
6862 TAACAAAGAGCACGAGACGTGCTAAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCACAAGA-GTGCTAAACAGAGAGCACACACAGTGCTA
*
6909 AACAGAGGGCACAAGCAGTGCTAAACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACAAG-AGTGCTAAACAGAGAGCACACACAGTGCTA
*
6955 ATCAGAGAGC
1 AACAGAGAGC
6965 GCGCAAGTGT
Statistics
Matches: 119, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
39 18 0.15
40 3 0.03
41 11 0.09
42 1 0.01
46 58 0.49
47 4 0.03
48 24 0.20
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (45 bp):
AACAGAGAGCACAAGAGTGCTAAACAGAGAGCACACACAGTGCTA
Found at i:11408 original size:24 final size:24
Alignment explanation
Indices: 11381--11442 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
11371 TAATCATAAA
*
11381 GAAGAAGAAGAAGAACAACAAGTC
1 GAAGAAGAAGAAGAACAACAAGAC
* * *
11405 GAAGAAGAAGTACAAGAACAAGAC
1 GAAGAAGAAGAAGAACAACAAGAC
*
11429 GAAGAAGAGGAAGA
1 GAAGAAGAAGAAGA
11443 GGAAAATCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.58, C:0.10, G:0.29, T:0.03
Consensus pattern (24 bp):
GAAGAAGAAGAAGAACAACAAGAC
Found at i:11421 original size:12 final size:12
Alignment explanation
Indices: 11381--11436 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
11371 TAATCATAAA
*
11381 GAAGAAGAAGAA
1 GAAGAAGAAGAC
* * *
11393 GAACAACAAGTC
1 GAAGAAGAAGAC
11405 GAAGAAGAAGTAC
1 GAAGAAGAAG-AC
*
11418 -AAGAACAAGAC
1 GAAGAAGAAGAC
11429 GAAGAAGA
1 GAAGAAGA
11437 GGAAGAGGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
11 2 0.06
12 30 0.91
13 1 0.03
ACGTcount: A:0.59, C:0.11, G:0.27, T:0.04
Consensus pattern (12 bp):
GAAGAAGAAGAC
Found at i:15795 original size:21 final size:21
Alignment explanation
Indices: 15766--15835 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
15756 ACATCCAGGT
*
15766 CTTCTTCTTCTTCCACTTCCA
1 CTTCTTCTTCTTCTACTTCCA
* * *
15787 CTTCCTCTTCTAT-TTCTTCCT
1 CTTCTTCTTCT-TCTACTTCCA
*
15808 CTTCTTCTTCTTCTACCTCCA
1 CTTCTTCTTCTTCTACTTCCA
15829 CTTCTTC
1 CTTCTTC
15836 ATACTCCACC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.95
22 1 0.03
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.51
Consensus pattern (21 bp):
CTTCTTCTTCTTCTACTTCCA
Found at i:15818 original size:15 final size:15
Alignment explanation
Indices: 15765--15820 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
15755 AACATCCAGG
15765 TCTTCTTCTTCTTCC
1 TCTTCTTCTTCTTCC
* *
15780 ACTTC--C-ACTTCC
1 TCTTCTTCTTCTTCC
15792 TCTTCTAT-TTCTTCC
1 TCTTCT-TCTTCTTCC
15807 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
15821 TACCTCCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
12 9 0.28
13 1 0.03
14 1 0.03
15 21 0.66
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTCTTCTTCTTCC
Found at i:24422 original size:78 final size:81
Alignment explanation
Indices: 24290--24438 Score: 250
Period size: 78 Copynumber: 1.9 Consensus size: 81
24280 ATTAAATGAT
*
24290 TTAAGTGAATTTTTTTATTATTGAAACATTTCAATCACTCGCCACACAAACATCCAAATAATGGA
1 TTAAGTGAATTTTTTTATTATTGAAACATTCCAATCACTCGCCACACAAACATCCAAATAATGGA
24355 AGAAACGAACATCCGA
66 AGAAACGAACATCCGA
* *
24371 TTAAGTG-ATTTTTTT-TTATTG-AACATTCCAATCACTCGTCATACAAACATCCAAATAATGGA
1 TTAAGTGAATTTTTTTATTATTGAAACATTCCAATCACTCGCCACACAAACATCCAAATAATGGA
24433 AGAAAC
66 AGAAAC
24439 AAAATTCAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
78 44 0.68
79 6 0.09
80 8 0.12
81 7 0.11
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (81 bp):
TTAAGTGAATTTTTTTATTATTGAAACATTCCAATCACTCGCCACACAAACATCCAAATAATGGA
AGAAACGAACATCCGA
Found at i:29523 original size:2 final size:2
Alignment explanation
Indices: 29516--29543 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29506 TCTGCTCATA
29516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29544 TCTTAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32191 original size:22 final size:22
Alignment explanation
Indices: 32166--32208 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32156 TGATATGAGG
*
32166 TAAAAATT-ATATGTAATAATTT
1 TAAAAATTCA-ATATAATAATTT
32188 TAAAAATTCAATATAATAATT
1 TAAAAATTCAATATAATAATT
32209 AAATAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAAATTCAATATAATAATTT
Found at i:38021 original size:7 final size:7
Alignment explanation
Indices: 38005--38044 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
37995 GCATATATTG
38005 TGCTGGC
1 TGCTGGC
*
38012 TGCCGGC
1 TGCTGGC
38019 TGCTGGC
1 TGCTGGC
38026 TGCTGGC
1 TGCTGGC
*
38033 TGCTGCC
1 TGCTGGC
38040 TGCTG
1 TGCTG
38045 CATATCGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.40, T:0.28
Consensus pattern (7 bp):
TGCTGGC
Found at i:43147 original size:27 final size:27
Alignment explanation
Indices: 43103--43155 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
43093 CTGTCATGTT
*
43103 CTCCTCCTCCACCGTGGGCACCAGCTG
1 CTCCTCCTCCACCATGGGCACCAGCTG
* *
43130 CTCCTCCTCCTCCATGGGCACTAGCT
1 CTCCTCCTCCACCATGGGCACCAGCT
43156 ACTGCCCCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.11, C:0.47, G:0.19, T:0.23
Consensus pattern (27 bp):
CTCCTCCTCCACCATGGGCACCAGCTG
Found at i:56371 original size:22 final size:22
Alignment explanation
Indices: 56320--56371 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
56310 ATGTTACGAA
*
56320 AATAAAGTTTAATAAAATATTT
1 AATAAAGTTTAATAAAATAGTT
* *
56342 TATAAAGTTTAAT-ATATAGTT
1 AATAAAGTTTAATAAAATAGTT
56363 AATATAAGT
1 AATA-AAGT
56372 ATGTTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (22 bp):
AATAAAGTTTAATAAAATAGTT
Found at i:56769 original size:2 final size:2
Alignment explanation
Indices: 56764--56797 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56754 TCATATTTCA
56764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56798 GCAAAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59515 original size:11 final size:11
Alignment explanation
Indices: 59499--59524 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59489 AAACCACTGC
59499 CAATAACAATA
1 CAATAACAATA
59510 CAATAACAATA
1 CAATAACAATA
59521 CAAT
1 CAAT
59525 CCAATCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (11 bp):
CAATAACAATA
Found at i:59523 original size:5 final size:5
Alignment explanation
Indices: 59516--59551 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
59506 AATACAATAA
*
59516 CAATA CAATC CAATC CAATC CAATC CAATC CAATC C
1 CAATC CAATC CAATC CAATC CAATC CAATC CAATC C
59552 TGGGTGGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.19
Consensus pattern (5 bp):
CAATC
Found at i:63484 original size:110 final size:107
Alignment explanation
Indices: 63294--63514 Score: 406
Period size: 110 Copynumber: 2.0 Consensus size: 107
63284 CGGTCAGAAG
63294 GCAATAAGGTTCGTTCTTTTAAAACATAACTAGTATTCTTTCATATGATAAAAGCAAAACCAAGT
1 GCAATAAGGTTCGTTCTTTTAAAACATAACTAGTATTCTTTCATATGATAAAAGCAAAACCAAGT
63359 GGCTGTCTTCCATATGCTACATGTGTCTCATTATTACTGTAT
66 GGCTGTCTTCCATATGCTACATGTGTCTCATTATTACTGTAT
*
63401 GCAATAAGGTTCTTTCTTTTAAAACATAACTAGTAGTATTCTTTCATATGATAAAAGCAAAACCA
1 GCAATAAGGTTCGTTCTTTTAAAACATAAC---TAGTATTCTTTCATATGATAAAAGCAAAACCA
63466 AGTGGCTGTCTTCCATATGCTACATGTGTCTCATTATTACTGTAT
63 AGTGGCTGTCTTCCATATGCTACATGTGTCTCATTATTACTGTAT
63511 GCAA
1 GCAA
63515 GAAGCAGCCT
Statistics
Matches: 110, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
107 29 0.26
110 81 0.74
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (107 bp):
GCAATAAGGTTCGTTCTTTTAAAACATAACTAGTATTCTTTCATATGATAAAAGCAAAACCAAGT
GGCTGTCTTCCATATGCTACATGTGTCTCATTATTACTGTAT
Done.