Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004100.1 Kokia drynarioides strain JFW-HI SEQ_117272, 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: 15429
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:190 original size:21 final size:21
Alignment explanation
Indices: 158--204 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
148 TTCAAAAAAA
* *
158 GTCAACGATCAACTGTCGATG
1 GTCAACGATCAACTGTCAACG
*
179 GTCAAC-AGTCAATTGTCAACG
1 GTCAACGA-TCAACTGTCAACG
200 GTCAA
1 GTCAA
205 TGGACAACGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
GTCAACGATCAACTGTCAACG
Found at i:212 original size:14 final size:14
Alignment explanation
Indices: 166--216 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
156 AAGTCAACGA
* *
166 TCAACTGTCGATGG
1 TCAACGGTCAATGG
* *
180 TCAACAGTCAATTG
1 TCAACGGTCAATGG
194 TCAACGGTCAATGG
1 TCAACGGTCAATGG
*
208 ACAACGGTC
1 TCAACGGTC
217 GGGTCAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (14 bp):
TCAACGGTCAATGG
Found at i:429 original size:7 final size:7
Alignment explanation
Indices: 419--472 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
409 ATTCTCAAAA
419 GTCAACG
1 GTCAACG
426 GTCAACG
1 GTCAACG
*
433 GTCAACT
1 GTCAACG
*
440 GTCAATG
1 GTCAACG
*
447 GTCAACA
1 GTCAACG
* **
454 ATCAATT
1 GTCAACG
461 GTCAACG
1 GTCAACG
468 GTCAA
1 GTCAA
473 TGGACAACAG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (7 bp):
GTCAACG
Found at i:436 original size:14 final size:14
Alignment explanation
Indices: 419--480 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
409 ATTCTCAAAA
*
419 GTCAACGGTCAACG
1 GTCAACGGTCAATG
*
433 GTCAACTGTCAATG
1 GTCAACGGTCAATG
** *
447 GTCAACAATCAATT
1 GTCAACGGTCAATG
461 GTCAACGGTCAATG
1 GTCAACGGTCAATG
*
475 GACAAC
1 GTCAAC
481 AGTCGGGTCA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (14 bp):
GTCAACGGTCAATG
Found at i:443 original size:21 final size:21
Alignment explanation
Indices: 419--472 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
409 ATTCTCAAAA
**
419 GTCAACGGTCAACGGTCAACT
1 GTCAACGGTCAACAATCAACT
* *
440 GTCAATGGTCAACAATCAATT
1 GTCAACGGTCAACAATCAACT
461 GTCAACGGTCAA
1 GTCAACGGTCAA
473 TGGACAACAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
GTCAACGGTCAACAATCAACT
Found at i:652 original size:268 final size:268
Alignment explanation
Indices: 158--685 Score: 905
Period size: 268 Copynumber: 2.0 Consensus size: 268
148 TTCAAAAAAA
* * *
158 GTCAACGATCAACTGTCGATGGTCAACAGTCAATTGTCAACGGTCAATGGACAACGGTCGGGTCA
1 GTCAACGATCAACTGTCAATGGTCAACAATCAATTGTCAACGGTCAATGGACAACAGTCGGGTCA
223 AATCGAATTGGGTTTAGGGTTTGGGTGATTTAGTTTTAAGGTTTGGGTATTGGGTTTTCCTGGTT
66 AATCGAATTGGGTTTAGGGTTTGGGTGATTTAGTTTTAAGGTTTGGGTATTGGGTTTTCCTGGTT
* * *
288 TTGGGTTTACACACACACTTAGGTAAATGACTTGGGGCTTAGTTTGGGTTTTGTTTAGGTTTGTT
131 TTGGATTTACACACACACTTAGGTAAATGACTTGGGGCTTAGTTTGAGTTTGGTTTAGGTTTGTT
* * *
353 GGGTAATAAAGGATTGAGTTAAGAACATTGGAAATTGGGTTGCTAAGGTTGGCGCAATTCTCAAA
196 GGGTAATAAAGCATTGAGTTAAAAACATTGGAAATTGGGTTGCTAAGGTTGGCCCAATTCTCAAA
418 AGTCAACG
261 AGTCAACG
*
426 GTCAACGGTCAACTGTCAATGGTCAACAATCAATTGTCAACGGTCAATGGACAACAGTCGGGTCA
1 GTCAACGATCAACTGTCAATGGTCAACAATCAATTGTCAACGGTCAATGGACAACAGTCGGGTCA
* *
491 AATCGAATTGGGTTTAGGGTTTGGGTGATTTAGTTTTAGGGTTTGGGTATTGGGTTTTCTTGGTT
66 AATCGAATTGGGTTTAGGGTTTGGGTGATTTAGTTTTAAGGTTTGGGTATTGGGTTTTCCTGGTT
* *
556 TTGGATTTACACACACACTTGGGTAAATGACTTGGGGCTTAGTTTGAGTTTGGTTTGGGTTTGTT
131 TTGGATTTACACACACACTTAGGTAAATGACTTGGGGCTTAGTTTGAGTTTGGTTTAGGTTTGTT
*
621 GGGTAAT-AAGCATTGAGTTAAAAACCATTGGAAATTGGGTTGCTAAGGTTGTCCCAATTCTCAA
196 GGGTAATAAAGCATTGAGTTAAAAA-CATTGGAAATTGGGTTGCTAAGGTTGGCCCAATTCTCAA
685 A
260 A
686 CTTTTAGTAA
Statistics
Matches: 244, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
267 15 0.06
268 229 0.94
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.34
Consensus pattern (268 bp):
GTCAACGATCAACTGTCAATGGTCAACAATCAATTGTCAACGGTCAATGGACAACAGTCGGGTCA
AATCGAATTGGGTTTAGGGTTTGGGTGATTTAGTTTTAAGGTTTGGGTATTGGGTTTTCCTGGTT
TTGGATTTACACACACACTTAGGTAAATGACTTGGGGCTTAGTTTGAGTTTGGTTTAGGTTTGTT
GGGTAATAAAGCATTGAGTTAAAAACATTGGAAATTGGGTTGCTAAGGTTGGCCCAATTCTCAAA
AGTCAACG
Found at i:1817 original size:27 final size:27
Alignment explanation
Indices: 1776--1956 Score: 151
Period size: 27 Copynumber: 6.9 Consensus size: 27
1766 GTTGGAGGAG
* *
1776 TATTTTGATTTTGGCTCATAAAAGTGA
1 TATTTTGATTCTGGCTCATAAGAGTGA
* * **
1803 TATTCTGATTCTGGCTCGTAAGAACGA
1 TATTTTGATTCTGGCTCATAAGAGTGA
*
1830 TATTTTGATTATGGCTCATAAGA-TCGA
1 TATTTTGATTCTGGCTCATAAGAGT-GA
* * * ** *
1857 TATTCTGATTTTAGCTTGTAAGAGTAA
1 TATTTTGATTCTGGCTCATAAGAGTGA
*
1884 TATTTTG--TCTGGGTCATAAGAGTGA
1 TATTTTGATTCTGGCTCATAAGAGTGA
* *
1909 TATTCTGA--CTGGCTCATAAGAGCGA
1 TATTTTGATTCTGGCTCATAAGAGTGA
1934 TATTTTG--TCTGGGCTCATAAGAG
1 TATTTTGATTCT-GGCTCATAAGAG
1957 CTAAACTCTG
Statistics
Matches: 122, Mismatches: 27, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
25 41 0.34
26 12 0.10
27 68 0.56
28 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (27 bp):
TATTTTGATTCTGGCTCATAAGAGTGA
Found at i:1839 original size:54 final size:53
Alignment explanation
Indices: 1776--1956 Score: 190
Period size: 54 Copynumber: 3.4 Consensus size: 53
1766 GTTGGAGGAG
* *
1776 TATTTTGATTTTGGCTCATAAAAGTGATATTCTGATTCTGGCTCGTAAGAACGA
1 TATTTTG-TTTTGGCTCATAAGAGTGATATTCTGATTCTGGCTCGTAAGAGCGA
* * * * **
1830 TATTTTGATTATGGCTCATAAGA-TCGATATTCTGATTTTAGCTTGTAAGAGTAA
1 TATTTTG-TTTTGGCTCATAAGAGT-GATATTCTGATTCTGGCTCGTAAGAGCGA
* * *
1884 TATTTTG-TCTGGGTCATAAGAGTGATATTCTGA--CTGGCTCATAAGAGCGA
1 TATTTTGTTTTGGCTCATAAGAGTGATATTCTGATTCTGGCTCGTAAGAGCGA
* *
1934 TATTTTGTCTGGGCTCATAAGAG
1 TATTTTGTTTTGGCTCATAAGAG
1957 CTAAACTCTG
Statistics
Matches: 104, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
50 18 0.17
51 11 0.11
52 22 0.21
53 2 0.02
54 51 0.49
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (53 bp):
TATTTTGTTTTGGCTCATAAGAGTGATATTCTGATTCTGGCTCGTAAGAGCGA
Found at i:1906 original size:25 final size:25
Alignment explanation
Indices: 1875--1956 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 25
1865 TTTTAGCTTG
*
1875 TAAGAGTAATATTTTGTCTGGGTCA
1 TAAGAGTGATATTTTGTCTGGGTCA
* * *
1900 TAAGAGTGATATTCTGACTGGCTCA
1 TAAGAGTGATATTTTGTCTGGGTCA
*
1925 TAAGAGCGATATTTTGTCTGGGCTCA
1 TAAGAGTGATATTTTGTCTGGG-TCA
1951 TAAGAG
1 TAAGAG
1957 CTAAACTCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 39 0.81
26 9 0.19
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (25 bp):
TAAGAGTGATATTTTGTCTGGGTCA
Found at i:1955 original size:26 final size:26
Alignment explanation
Indices: 1788--1975 Score: 114
Period size: 27 Copynumber: 7.2 Consensus size: 26
1778 TTTTGATTTT
* *
1788 GGCTCATAAAAGTGATATTCTGATTCT-
1 GGCTCATAAGAGCGATATTCTG--TCTG
* * * *
1815 GGCTCGTAAGAACGATATTTTGAT-TAT
1 GGCTCATAAGAGCGATATTCTG-TCT-G
* * *
1842 GGCTCATAAGATCGATATTCTGATTTT
1 GGCTCATAAGAGCGATATTCTG-TCTG
* ** ** *
1869 AGCTTGTAAGAGTAATATTTTGTCTG
1 GGCTCATAAGAGCGATATTCTGTCTG
* *
1895 GG-TCATAAGAGTGATATTCTGACT-
1 GGCTCATAAGAGCGATATTCTGTCTG
*
1919 GGCTCATAAGAGCGATATTTTGTCTG
1 GGCTCATAAGAGCGATATTCTGTCTG
* * *
1945 GGCTCATAAGAGCTAAACTCTGTCTG
1 GGCTCATAAGAGCGATATTCTGTCTG
1971 GGCTC
1 GGCTC
1976 GTATAAGCTA
Statistics
Matches: 125, Mismatches: 31, Indels: 11
0.75 0.19 0.07
Matches are distributed among these distances:
24 2 0.02
25 37 0.30
26 31 0.25
27 54 0.43
28 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (26 bp):
GGCTCATAAGAGCGATATTCTGTCTG
Found at i:3280 original size:27 final size:28
Alignment explanation
Indices: 3221--3278 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3211 TACTGGTAGG
3221 AAACTACAGTTTTTTTTGAAAGCTTATT
1 AAACTACAGTTTTTTTTGAAAGCTTATT
3249 AAACTACAGTTTTTTTTGAAAGCTTATT
1 AAACTACAGTTTTTTTTGAAAGCTTATT
3277 AA
1 AA
3279 CTTGATATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (28 bp):
AAACTACAGTTTTTTTTGAAAGCTTATT
Found at i:7718 original size:9 final size:9
Alignment explanation
Indices: 7704--7743 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
7694 AATCCATTTT
7704 TCTCCATTC
1 TCTCCATTC
7713 TCTCCATTC
1 TCTCCATTC
* *
7722 TTTCAATTC
1 TCTCCATTC
*
7731 TCTCTATTC
1 TCTCCATTC
7740 TCTC
1 TCTC
7744 AAGATTAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.12, C:0.38, G:0.00, T:0.50
Consensus pattern (9 bp):
TCTCCATTC
Found at i:8940 original size:21 final size:21
Alignment explanation
Indices: 8916--8974 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
8906 CTACCAGTAG
*
8916 AACTAAGACATCTATCGATAC
1 AACTAAGACTTCTATCGATAC
**
8937 AACTCTGTA-TTCTATCGATAC
1 AACTAAG-ACTTCTATCGATAC
*
8958 AACCAAGACTTCTATCG
1 AACTAAGACTTCTATCG
8975 GTAGAACATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (21 bp):
AACTAAGACTTCTATCGATAC
Found at i:13429 original size:3 final size:3
Alignment explanation
Indices: 13421--13446 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13411 AGTTGGTAGC
13421 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
13447 TTCAAGGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.