Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010366.1 Kokia drynarioides strain JFW-HI SEQ_125238, 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: 13490
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Found at i:60 original size:6 final size:6
Alignment explanation
Indices: 14--141 Score: 108
Period size: 6 Copynumber: 22.0 Consensus size: 6
4 TGGGTTTTAT
* * *
14 TTTAAA TTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
62 TTTAAA -ATAAA TTTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
108 TTTTAAA --CAAA TTTAAT TTTAAA -ATAAA TTTAAA
1 -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
142 GGGAGTATAG
Statistics
Matches: 97, Mismatches: 15, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.03
5 19 0.20
6 60 0.62
7 15 0.15
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:61 original size:17 final size:17
Alignment explanation
Indices: 15--110 Score: 104
Period size: 17 Copynumber: 5.5 Consensus size: 17
5 GGGTTTTATT
15 TTAAATTTTAAATTTGAAA
1 TTAAA-TTTAAATTT-AAA
* * *
34 ATAATTTTAAACTTAAA
1 TTAAATTTAAATTTAAA
51 TTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
*
68 ATAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
*
85 TTTAAA-ATAAATTTAAA
1 -TTAAATTTAAATTTAAA
102 TTTAAATTT
1 -TTAAATTT
111 TAAACAAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
17 49 0.75
18 13 0.20
19 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:77 original size:23 final size:23
Alignment explanation
Indices: 47--130 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
37 ATTTTAAACT
47 TAAA-TTAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAATTTAAAA
69 TAAATTTAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAATTTAAAA
*
92 TAAATTTAAATTTAAATTTTAAA
1 TAAATTTAAATTTAAATTTAAAA
* *
115 CAAATTTAATTTTAAA
1 TAAATTTAAATTTAAA
131 ATAAATTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
22 4 0.07
23 54 0.93
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTTAAAA
Found at i:90 original size:40 final size:39
Alignment explanation
Indices: 39--141 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 39
29 TGAAAATAAT
* * *
39 TTTAAACTTAAATTAAATTTAAATTTAAA-ATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAATATAAA--CAAA
*
79 TTTAAATTTAAAATAAATTTAAATTTAAATTTTAAACAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAA-TATAAACAAA
*
119 TTTAATTTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAA
142 GGGAGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 52 0.93
42 4 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (39 bp):
TTTAAATTTAAAATAAATTTAAATTTAAATATAAACAAA
Found at i:119 original size:17 final size:18
Alignment explanation
Indices: 99--141 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
89 AAATAAATTT
99 AAATTTAAATTTT-AAAC
1 AAATTTAAATTTTAAAAC
*
116 AAATTT-AATTTTAAAAT
1 AAATTTAAATTTTAAAAC
133 AAATTTAAA
1 AAATTTAAA
142 GGGAGTATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 15 0.65
18 2 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTAAATTTTAAAAC
Found at i:925 original size:206 final size:206
Alignment explanation
Indices: 522--1081 Score: 564
Period size: 206 Copynumber: 2.7 Consensus size: 206
512 TGTGTAGTTT
* * * * *
522 GTTTCAAT-TCGCTTCTCTGTATCTCATCAGGAAGATGAATTTTGATCAACTTCTCCA-TATCTC
1 GTTTCAATCT-GCCTCTCTGCATCTCATCAGGAAGACGAATTTGGTTC-ACTTCT-CAGTATCTC
* * ** * * * * ** * *
585 ATCAGGAAGCTAATCGTTTTATTATTTTGCCCTGCTTCTCAATATCTTATCATAAAGATGGGGTT
63 ATAAGGAAGCTAACCG-TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTT
* * * * * * * * *
650 CGAAGGTTTAT--TC--ATCGTGCGTGGGTTTGGTTTGGCCTTCTTCTCAGTATCTAATCGGGAA
127 CAAAGATTT-TGCTCGTTTCGAGCGTAGGCTTGATTTGGCCTTCTTCTCAGTATCTAATAGAGAA
*
711 GATGACCGCATCACTT
191 GATGACCGCATCACTC
*
727 GTTTCAATCTGCCTCTCCT-CATCTCATTAGGAAGACGAATTTGGTTCACTTCTCTA-TATCTCA
1 GTTTCAATCTGCCTCT-CTGCATCTCATCAGGAAGACGAATTTGGTTCACTTCTC-AGTATCTCA
** * * * *
790 TCTGGAAGCTAACCGTTTATTGCTTCGACTTGCTTCTCGGTATCTCATCAGGAAGCTGGGGTTCG
64 TAAGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCA
* *
855 AAGATTTTGCTCGCTTT-GAGCGTAGGCTTGATTTGGTCTTCTTCTCAGTATCTCATTAGAG-AG
129 AAGATTTTGCTCG-TTTCGAGCGTAGGCTTGATTTGGCCTTCTTCTCAGTATCT-AATAGAGAAG
*
918 ATGACCGCATCGCTC
192 ATGACCGCATCACTC
* * ** *
933 GTTTCAATCTGCTTCTCTGTATCTCATCAGGAAGGTGGATTTGGTTCACTTCTCAGTATCTCATA
1 GTTTCAATCTGCCTCTCTGCATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATA
* * *
998 AGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGAGGTTCAAA
66 AGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAA
1063 GATTTTGCTCGTTTCGAGC
131 GATTTTGCTCGTTTCGAGC
1082 CTCATTTGGG
Statistics
Matches: 297, Mismatches: 46, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
202 1 0.00
203 46 0.15
204 29 0.10
205 42 0.14
206 174 0.59
207 5 0.02
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (206 bp):
GTTTCAATCTGCCTCTCTGCATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATA
AGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAA
GATTTTGCTCGTTTCGAGCGTAGGCTTGATTTGGCCTTCTTCTCAGTATCTAATAGAGAAGATGA
CCGCATCACTC
Found at i:12805 original size:29 final size:28
Alignment explanation
Indices: 12773--13306 Score: 316
Period size: 29 Copynumber: 18.1 Consensus size: 28
12763 AAATGGTAAC
* *
12773 TTTGGAAGGTTCAGAGTTAAAATGGGATT
1 TTTGGAAGGTTC-GGGTTAAAATGGAATT
*
12802 TTTGGAA-GTTCGTGGGTAAAATGGTAATT
1 TTTGGAAGGTTCG-GGTTAAAATGG-AATT
* *
12831 TTCGGAAGGTTCGGGGTCAAAAATGG-ATT
1 TTTGGAAGGTTC-GGGT-TAAAATGGAATT
* * *
12860 TTTGG-AGGTTCGAGGGTAATATAGTAATT
1 TTTGGAAGGTTCG-GGTTAAAAT-GGAATT
* * *
12889 TTTAGAAGGTTCGAGGTAAAAAATGGGATT
1 TTTGGAAGGTTCG-GGT-TAAAATGGAATT
* *
12919 TTTGGAA-GTTCGAGGGTAAAATGATAATT
1 TTTGGAAGGTTCG-GGTTAAAATG-GAATT
* * * *
12948 TTTGAAAGGTTTGGGGTCAAAAATGGGATT
1 TTTGGAAGG-TTCGGGT-TAAAATGGAATT
*
12978 TTTGG-AGGTTCGAGGGTAAAATGGTAA-T
1 TTTGGAAGGTTCG-GGTTAAAATGG-AATT
*
13006 TTTAGAAGGTTCGAGGTTAAAAATGGAATT
1 TTTGGAAGGTTCG-GGTT-AAAATGGAATT
**
13036 TTTGGAA-GTTCAGGGAGAAAATGGTAATT
1 TTTGGAAGGTTC-GGGTTAAAATGG-AATT
* * *
13065 TTTAGAAGGTTCGGGTAAAAAAAATGGGATT
1 TTTGGAAGGTTCGGGT---TAAAATGGAATT
**
13096 TTTGGAA-GTTCGGGGGCAAAATGGTAATT
1 TTTGGAAGGTTC-GGGTTAAAATGG-AATT
* * *
13125 TTTAGAAGGTTTGGGTTCAAAAATGGGATT
1 TTTGGAAGGTTCGGGTT--AAAATGGAATT
*
13155 TTTGGAA-GTTCGAGGGTAAAAATGGTAATT
1 TTTGGAAGGTTC--GGGTTAAAATGG-AATT
* * *
13185 TTTAGAAGGTTCGGGGTCAAAGATGGGATT
1 TTTGGAAGGTTC-GGGTTAAA-ATGGAATT
13215 TTTGGAA-GTTCGGGTGTAAAAATGGTAATT
1 TTTGGAAGGTTCGGGT-T-AAAATGG-AATT
* * *
13245 TTTAGAAGGTTTGGGTTCAAAAATGGGATT
1 TTTGGAAGGTTCGGGTT--AAAATGGAATT
*
13275 TTTGGAA-GTTCGAGGGTAAAATGGTAATT
1 TTTGGAAGGTTCG-GGTTAAAATGG-AATT
13304 TTT
1 TTT
13307 AAAAGGTTTA
Statistics
Matches: 394, Mismatches: 69, Indels: 84
0.72 0.13 0.15
Matches are distributed among these distances:
27 6 0.02
28 68 0.17
29 125 0.32
30 121 0.31
31 67 0.17
32 7 0.02
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTGGAAGGTTCGGGTTAAAATGGAATT
Found at i:12901 original size:30 final size:29
Alignment explanation
Indices: 12799--13306 Score: 193
Period size: 30 Copynumber: 17.2 Consensus size: 29
12789 TTAAAATGGG
* *
12799 ATTTTTGGAA-GTTCGTGGGTAAAATGGTA
1 ATTTTT-GAAGGTTCGAGGGTAAAATAGTA
* *
12828 ATTTTCGGAAGGTTCG-GGGTCAAAA-A-TGG
1 ATTTT-TGAAGGTTCGAGGGT-AAAATAGT-A
* *
12857 ATTTTTGGAGGTTCGAGGGTAATATAGTA
1 ATTTTTGAAGGTTCGAGGGTAAAATAGTA
* **
12886 ATTTTTAGAAGGTTCGA-GGTAAAAAATGGG
1 ATTTTT-GAAGGTTCGAGGGTAAAATA-GTA
12916 ATTTTTGGAA-GTTCGAGGGTAAAAT-GATA
1 ATTTTT-GAAGGTTCGAGGGTAAAATAG-TA
* **
12945 ATTTTTGAAAGGTTTG-GGGTCAAAA-ATGGG
1 ATTTTTG-AAGGTTCGAGGGT-AAAATA-GTA
* *
12975 ATTTTTGGAGGTTCGAGGGTAAAATGGTA
1 ATTTTTGAAGGTTCGAGGGTAAAATAGTA
* * *
13004 ATTTTAGAAGGTTCGAGGTTAAAA-ATGGA
1 ATTTTTGAAGGTTCGAGGGTAAAATA-GTA
* *
13033 ATTTTTGGAA-GTTC-AGGGAGAAAATGGTA
1 ATTTTT-GAAGGTTCGAGGG-TAAAATAGTA
* **
13062 ATTTTTAGAAGGTTC--GGGTAAAAAAAATGGG
1 ATTTTT-GAAGGTTCGAGGGT--AAAATA-GTA
* * *
13093 ATTTTTGGAA-GTTCGGGGGCAAAATGGTA
1 ATTTTT-GAAGGTTCGAGGGTAAAATAGTA
* * **
13122 ATTTTTAGAAGGTTTG-GGTTCAAAA-ATGGG
1 ATTTTT-GAAGGTTCGAGGGT-AAAATA-GTA
*
13152 ATTTTTGGAA-GTTCGAGGGTAAAAATGGTA
1 ATTTTT-GAAGGTTCGAGGGT-AAAATAGTA
**
13182 ATTTTTAGAAGGTTCG-GGGTCAAAGAT-GGG
1 ATTTTT-GAAGGTTCGAGGGT-AAA-ATAGTA
*
13212 ATTTTTGGAA-GTTCG-GGTGTAAAAATGGTA
1 ATTTTT-GAAGGTTCGAGG-GT-AAAATAGTA
* * **
13242 ATTTTTAGAAGGTTTG-GGTTCAAAA-ATGGG
1 ATTTTT-GAAGGTTCGAGGGT-AAAATA-GTA
*
13272 ATTTTTGGAA-GTTCGAGGGTAAAATGGTA
1 ATTTTT-GAAGGTTCGAGGGTAAAATAGTA
13301 ATTTTT
1 ATTTTT
13307 AAAAGGTTTA
Statistics
Matches: 357, Mismatches: 81, Indels: 82
0.69 0.16 0.16
Matches are distributed among these distances:
28 17 0.05
29 154 0.43
30 159 0.45
31 24 0.07
32 3 0.01
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (29 bp):
ATTTTTGAAGGTTCGAGGGTAAAATAGTA
Found at i:12947 original size:59 final size:58
Alignment explanation
Indices: 12757--13314 Score: 707
Period size: 60 Copynumber: 9.5 Consensus size: 58
12747 CTGACGCACA
* * * * *
12757 AGGGCAAAATGGTAA-CTTTGGAAGGTTCAGAGT-TAAAATGGGATTTTTGGAAGTTCG
1 AGGGTAAAATGGTAATTTTTAGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTTCG
* ** *
12814 TGGGTAAAATGGTAATTTTCGGAAGGTTCGGGGTCAAAAAT-GGATTTTTGGAGGTTCG
1 AGGGTAAAATGGTAATTTTTAGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTTCG
* * *
12872 AGGGTAATATAGTAATTTTTAGAAGGTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCG
1 AGGGTAAAATGGTAATTTTTAGAAGGTTCG-GGTCAAAAATGGGATTTTTGGAAGTTCG
* * *
12931 AGGGTAAAATGATAATTTTT-GAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAGGTTCG
1 AGGGTAAAATGGTAATTTTTAG-AAGG-TTCGGGTCAAAAATGGGATTTTTGGAAGTTCG
* *
12990 AGGGTAAAATGGTAA-TTTTAGAAGGTTCGAGGTTAAAAATGGAATTTTTGGAAGTTC-
1 AGGGTAAAATGGTAATTTTTAGAAGGTTCG-GGTCAAAAATGGGATTTTTGGAAGTTCG
* *
13047 AGGGAGAAAATGGTAATTTTTAGAAGGTTCGGGTAAAAAAAATGGGATTTTTGGAAGTTCG
1 AGGG-TAAAATGGTAATTTTTAGAAGGTTCGGGT--CAAAAATGGGATTTTTGGAAGTTCG
* * *
13108 GGGGCAAAATGGTAATTTTTAGAAGGTTTGGGTTCAAAAATGGGATTTTTGGAAGTTCG
1 AGGGTAAAATGGTAATTTTTAGAAGGTTCGGG-TCAAAAATGGGATTTTTGGAAGTTCG
*
13167 AGGGTAAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAGATGGGATTTTTGGAAGTTCG
1 AGGGT-AAAATGGTAATTTTTAGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTTCG
*
13227 -GGTGTAAAAATGGTAATTTTTAGAAGGTTTGGGTTCAAAAATGGGATTTTTGGAAGTTCG
1 AGG-GT-AAAATGGTAATTTTTAGAAGGTTCGGG-TCAAAAATGGGATTTTTGGAAGTTCG
*
13287 AGGGTAAAATGGTAATTTTTAAAAGGTT
1 AGGGTAAAATGGTAATTTTTAGAAGGTT
13315 TAGGGACCTC
Statistics
Matches: 442, Mismatches: 40, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
57 21 0.05
58 109 0.25
59 151 0.34
60 152 0.34
61 9 0.02
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCG
Done.