Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004730.1 Kokia drynarioides strain JFW-HI SEQ_118310, 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: 31305
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:2019 original size:22 final size:22
Alignment explanation
Indices: 1980--2021 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1970 TATATGGGAT
1980 TTTTTCTAAAAAATTAATTTAA
1 TTTTTCTAAAAAATTAATTTAA
*
2002 TTTTTC-AAAAATTATAATTT
1 TTTTTCTAAAAAAT-TAATTT
2022 TCTACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTTCTAAAAAATTAATTTAA
Found at i:4291 original size:8 final size:8
Alignment explanation
Indices: 4274--4319 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
4264 GTCAGAAAAT
4274 AACAACAA
1 AACAACAA
*
4282 AACAATAA
1 AACAACAA
4290 AA-AA-AA
1 AACAACAA
* *
4296 ATCAAGAA
1 AACAACAA
4304 AACAACAA
1 AACAACAA
4312 AACAACAA
1 AACAACAA
4320 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 3 0.09
7 4 0.12
8 25 0.78
ACGTcount: A:0.76, C:0.17, G:0.02, T:0.04
Consensus pattern (8 bp):
AACAACAA
Found at i:5870 original size:6 final size:6
Alignment explanation
Indices: 5859--5883 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5849 CTTTGTTACT
5859 TCTTCA TCTTCA TCTTCA TCTTCA T
1 TCTTCA TCTTCA TCTTCA TCTTCA T
5884 GCCAATCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:23204 original size:96 final size:96
Alignment explanation
Indices: 23023--23206 Score: 248
Period size: 96 Copynumber: 1.9 Consensus size: 96
23013 TAAAGAATGT
**
23023 TCGATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAA
1 TCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAA
* *
23088 GATAATGAAACATTGTCTCGATTAAGGGTAA
66 GATAAAGAAACATTGCCTCGATTAAGGGTAA
* * *
23119 TCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-TGAAACTCG
1 TCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCG
*
23183 AA-ATAAA-AGAATATTGCCTCGATT
64 AAGATAAAGA-AACATTGCCTCGATT
23207 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 70 0.91
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
TCGATTATCTCGATTCGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAA
GATAAAGAAACATTGCCTCGATTAAGGGTAA
Found at i:23726 original size:29 final size:28
Alignment explanation
Indices: 23578--23902 Score: 160
Period size: 29 Copynumber: 11.1 Consensus size: 28
23568 GGACATCCAG
**
23578 GGGT-AAAATGGTAATTTTTAGGAA-AATA
1 GGGTCAAAATGG-AATTTTT-GGAATTTTA
* * **
23606 GGGATCAATATGAAATTTTTGGATATTTGG
1 GGG-TCAAAATGGAATTTTTGGA-ATTTTA
* * *
23636 GGGT-AAAAGGGTAATTTTTGAAAGTTTCGA
1 GGGTCAAAATGG-AATTTTTGGAA-TTT-TA
* * * ***
23666 GGTTAAAAATGGAACTTTTGGACATACGA
1 GGGTCAAAATGGAATTTTTGGA-ATTTTA
23695 GGG-CAAAATGGTAATTTTTGGTAATTTTA
1 GGGTCAAAATGG-AATTTTTGG-AATTTTA
* * *
23724 GGGTCAAAAATAGAATTTTTGGAAGTTTC
1 GGGTC-AAAATGGAATTTTTGGAATTTTA
* * *
23753 GGAGTTAAAAATGAAATTTTTGGACA-TTCA
1 GG-G-TCAAAATGGAATTTTTGGA-ATTTTA
23783 GGGGT-AAAATGGTAATTTTTGGAAGTTTTA
1 -GGGTCAAAATGG-AATTTTTGGAA-TTTTA
*
23813 GGGTCAAAATGGAATTTTTAGG-AGTTTA
1 GGGTCAAAATGGAATTTTT-GGAATTTTA
* ** * *
23841 GGGGTAAAAATATAATTTTTGGAAGTTTC
1 -GGGTCAAAATGGAATTTTTGGAATTTTA
*
23870 GTGGTCAAAATGGAATTTTTGGATAGTTTA
1 G-GGTCAAAATGGAATTTTTGGA-ATTTTA
23900 GGG
1 GGG
23903 ACCTCAAGGG
Statistics
Matches: 229, Mismatches: 42, Indels: 51
0.71 0.13 0.16
Matches are distributed among these distances:
28 32 0.14
29 111 0.48
30 69 0.30
31 17 0.07
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
GGGTCAAAATGGAATTTTTGGAATTTTA
Found at i:23741 original size:30 final size:28
Alignment explanation
Indices: 23694--23902 Score: 183
Period size: 29 Copynumber: 7.1 Consensus size: 28
23684 TGGACATACG
*
23694 AGGG-CAAAATGGTAATTTTTGGTAATTTT
1 AGGGTCAAAATGG-AATTTTTGG-AAGTTT
*
23723 AGGGTCAAAAATAGAATTTTTGGAAGTTT
1 AGGGTC-AAAATGGAATTTTTGGAAGTTT
* * * *
23752 CGGAGTTAAAAATGAAATTTTTGGACA-TTC
1 AGG-G-TCAAAATGGAATTTTTGGA-AGTTT
23782 AGGGGT-AAAATGGTAATTTTTGGAAGTTTT
1 A-GGGTCAAAATGG-AATTTTTGGAAG-TTT
23812 AGGGTCAAAATGGAATTTTTAGG-AGTTT
1 AGGGTCAAAATGGAATTTTT-GGAAGTTT
* **
23840 AGGGGTAAAAATATAATTTTTGGAAGTTT
1 A-GGGTCAAAATGGAATTTTTGGAAGTTT
*
23869 CGTGGTCAAAATGGAATTTTTGGATAGTTT
1 AG-GGTCAAAATGGAATTTTTGGA-AGTTT
23899 AGGG
1 AGGG
23903 ACCTCAAGGG
Statistics
Matches: 147, Mismatches: 18, Indels: 30
0.75 0.09 0.15
Matches are distributed among these distances:
28 14 0.10
29 76 0.52
30 47 0.32
31 10 0.07
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
AGGGTCAAAATGGAATTTTTGGAAGTTT
Found at i:23750 original size:89 final size:88
Alignment explanation
Indices: 23648--23839 Score: 257
Period size: 89 Copynumber: 2.2 Consensus size: 88
23638 GTAAAAGGGT
* *
23648 AATTTTTGAAAGTTTC-GAGGTTAAAAATGGAACTTTTGGACATAC-GAGGGCAAAATGGTAATT
1 AATTTTTGGAAGTTTCGGA-GTTAAAAATGAAACTTTTGGACATACAG-GGGCAAAATGGTAATT
23711 TTTGGTAA-TTTTAGGGTCAAAAATAG
64 TTTGG-AAGTTTTAGGGTC-AAAATAG
* * *
23737 AATTTTTGGAAGTTTCGGAGTTAAAAATGAAATTTTTGGACATTCAGGGGTAAAATGGTAATTTT
1 AATTTTTGGAAGTTTCGGAGTTAAAAATGAAACTTTTGGACATACAGGGGCAAAATGGTAATTTT
*
23802 TGGAAGTTTTAGGGTCAAAATGG
66 TGGAAGTTTTAGGGTCAAAATAG
23825 AATTTTTAGG-AGTTT
1 AATTTTT-GGAAGTTT
23840 AGGGGTAAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
88 20 0.22
89 70 0.75
90 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (88 bp):
AATTTTTGGAAGTTTCGGAGTTAAAAATGAAACTTTTGGACATACAGGGGCAAAATGGTAATTTT
TGGAAGTTTTAGGGTCAAAATAG
Found at i:23829 original size:58 final size:56
Alignment explanation
Indices: 23698--23892 Score: 205
Period size: 58 Copynumber: 3.3 Consensus size: 56
23688 CATACGAGGG
* *
23698 CAAAATGGTAATTTTTGGTAATTTTA-GGGTCAAAAATAGAATTTTTGGAAGTTTCGGAGTT
1 CAAAATGG-AATTTTTGG-AA-TTCAGGGGT-AAAAATATAATTTTTGGAAGTTTCGG-G-T
* * * *
23759 AAAAATGAAATTTTTGGACATTCAGGGGT-AAAATGGTAATTTTTGGAAGTTTTAGGGT
1 CAAAATGGAATTTTTGGA-ATTCAGGGGTAAAAAT-ATAATTTTTGGAAG-TTTCGGGT
* *
23817 CAAAATGGAATTTTTAGGAGTTTAGGGGTAAAAATATAATTTTTGGAAGTTTCGTGGT
1 CAAAATGGAATTTTT-GGAATTCAGGGGTAAAAATATAATTTTTGGAAGTTTCG-GGT
23875 CAAAATGGAATTTTTGGA
1 CAAAATGGAATTTTTGGA
23893 TAGTTTAGGG
Statistics
Matches: 115, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
57 7 0.06
58 58 0.50
59 25 0.22
60 19 0.17
61 6 0.05
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (56 bp):
CAAAATGGAATTTTTGGAATTCAGGGGTAAAAATATAATTTTTGGAAGTTTCGGGT
Found at i:24975 original size:3 final size:3
Alignment explanation
Indices: 24967--25018 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
24957 TTATTGATAT
* * * * *
24967 TTA TTA TTA ATA ATA TTA TTA TTA TTG TTA TTTA TTA TAA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
25013 TTA TTA
1 TTA TTA
25019 ATGTCATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:24992 original size:31 final size:31
Alignment explanation
Indices: 24956--25018 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
24946 TTCTTTTTTG
24956 ATTATTGATATTTATTATTAA-TAATATTATT
1 ATTATTGATATTTATTA-TAATTAATATTATT
*
24987 ATTATTGTTATTTATTATAATTAATATTATT
1 ATTATTGATATTTATTATAATTAATATTATT
25018 A
1 A
25019 ATGTCATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
ATTATTGATATTTATTATAATTAATATTATT
Found at i:25775 original size:23 final size:23
Alignment explanation
Indices: 25744--25795 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
25734 AGTTTTGGAC
* * *
25744 ATTTTATTTGTAATTGGATTTTG
1 ATTTAATTTATAATTGGATTTTA
25767 ATTTAATTTATAATTGGATTTTA
1 ATTTAATTTATAATTGGATTTTA
25790 ATTTAA
1 ATTTAA
25796 ATAGATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.58
Consensus pattern (23 bp):
ATTTAATTTATAATTGGATTTTA
Found at i:25828 original size:17 final size:17
Alignment explanation
Indices: 25803--25865 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
25793 TAAATAGATT
*
25803 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
25820 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
25837 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
25854 TGAATTTAAATT
1 TAAATTTAAATT
25866 CTGTTGGGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28698 original size:161 final size:161
Alignment explanation
Indices: 28390--28849 Score: 618
Period size: 161 Copynumber: 2.8 Consensus size: 161
28380 GATATTAGTT
* * * * *
28390 TATGATTTATTAAATTTTAGAGCTTATCTTGATTTATGATTTTAACAATTGTAGCAGCCAATCAA
1 TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGCCAATCAA
* *
28455 GACCATCCTACTATCAAGATAGACCTTTGTGAATCAATGATTGCTGAAAAAGGTGGCCATTAAGA
66 GACCATCCTAC-ATCAGGATAGACCTTTGCGAATCAATGATTGCTGAAAAAGGTGGCCATTAAGA
* * *
28520 AACACAAGTAGTACAACACACTATTTCACCTG
130 AACACAAATAATACAACACACTATTTCACATG
**
28552 TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAATCAATCAA
1 TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGCCAATCAA
* * * *
28617 AACCATCTTACATCAGGATAAACCTTTGCGAATCAATAATTGCTGAAAAAGGTGGCCATTAAGAA
66 GACCATCCTACATCAGGATAGACCTTTGCGAATCAATGATTGCTGAAAAAGGTGGCCATTAAGAA
28682 ACACAAATAATACAACACACTATTTCACATG
131 ACACAAATAATACAACACACTATTTCACATG
* * * *
28713 TAT-AGTTTATTAAATTTTATATCATATTTTAATTTATTATTTTAACAGTTCT-GACAGCCAACC
1 TATGA-TTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAG-CAGCCAATC
* * * * * ***
28776 AAGACCATCCTACCACCAGAATAGACTTTTGCGAATAAATGATTACTGAAAAAGGTGATAATTAA
64 AAGACCATCCTA-CATCAGGATAGACCTTTGCGAATCAATGATTGCTGAAAAAGGTGGCCATTAA
28841 GAAACACAA
128 GAAACACAA
28850 GTAGTACTAC
Statistics
Matches: 261, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
160 2 0.01
161 141 0.54
162 118 0.45
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (161 bp):
TATGATTTATTAAATTTTATATCATATCTTAATTTATGATTTTAACAGTTGTAGCAGCCAATCAA
GACCATCCTACATCAGGATAGACCTTTGCGAATCAATGATTGCTGAAAAAGGTGGCCATTAAGAA
ACACAAATAATACAACACACTATTTCACATG
Done.