Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006674.1 Kokia drynarioides strain JFW-HI SEQ_121267, 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: 33861
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1313 original size:18 final size:16
Alignment explanation
Indices: 1281--1324 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
1271 ATGGAACGAG
1281 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
1297 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
1311 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
1325 ACCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:1653 original size:17 final size:18
Alignment explanation
Indices: 1631--1665 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1621 GGCTTAGGGT
*
1631 TTAAATTT-TTTTATTAA
1 TTAAATTTATTTAATTAA
1648 TTAAATTTATTTAATTAA
1 TTAAATTTATTTAATTAA
1666 AGATTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTATTTAATTAA
Found at i:2121 original size:75 final size:76
Alignment explanation
Indices: 2031--2171 Score: 194
Period size: 75 Copynumber: 1.9 Consensus size: 76
2021 AAAATCATCT
* * * * *
2031 TTGGTATATCCAACTAGAGCTGTGCTCACTATTGATATCATCA-GTTATTCGACTAGCGTTGGGC
1 TTGGTATATCCAACTACAGCAGAGCTCACTATTGATATCATCATGTTATCCGACTAGCGCTGGGC
2095 ACAAAACATTG
66 ACAAAACATTG
* ** *
2106 TTGGTATATCTAACTACAGCAGAGCTCACTATTGATATTGTCATTTTATCCGACTAGCGCTGGGC
1 TTGGTATATCCAACTACAGCAGAGCTCACTATTGATATCATCATGTTATCCGACTAGCGCTGGGC
2171 A
66 A
2172 TAACCTTCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
75 37 0.66
76 19 0.34
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (76 bp):
TTGGTATATCCAACTACAGCAGAGCTCACTATTGATATCATCATGTTATCCGACTAGCGCTGGGC
ACAAAACATTG
Found at i:2340 original size:145 final size:145
Alignment explanation
Indices: 2074--2389 Score: 386
Period size: 145 Copynumber: 2.2 Consensus size: 145
2064 GATATCATCA
* * * * * *
2074 GTTATTCGACTAGCGTTGGGCACAAAACATTGTTGGTATATCTAACTACAGCAGAGCTCACTATT
1 GTTATCCGACTAGCATTGGGCACAAAACATCGTTGGTATAACCAACTAAAGCAGAGCTCACTATT
* * *
2139 GATATTGTCATTTTATCCGACTAGCGCTGGGCATAACCTTCATCAGTTGAATTGACTAGTGATGG
66 GATATCGTCATTTTATCCGACTAGCGCTGGGCACAACCTTCATCAGTTGAACTGACTAGTGATGG
2204 GCACACAAATCGTCG
131 GCACACAAATCGTCG
* *
2219 GTTATCCGACTTGCATTGGGCACAAAACATCGTTGGTATAACCAACTAAAG-ATGGGCTCACTAT
1 GTTATCCGACTAGCATTGGGCACAAAACATCGTTGGTATAACCAACTAAAGCA-GAGCTCACTAT
* * ** * *
2283 TGATATCGTCGA-TTTATCCGACTAGCTCTGGGCGCAACCTTTGTCAGTTTAACTGACTAGTGTT
65 TGATATCGTC-ATTTTATCCGACTAGCGCTGGGCACAACCTTCATCAGTTGAACTGACTAGTGAT
* *
2347 GGGCACCCAAATCGTCA
129 GGGCACACAAATCGTCG
* * *
2364 ATTA-CCAGACTAACGTTGGGCACAAA
1 GTTATCC-GACTAGCATTGGGCACAAA
2390 CTTTGTTACG
Statistics
Matches: 145, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
144 3 0.02
145 141 0.97
146 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (145 bp):
GTTATCCGACTAGCATTGGGCACAAAACATCGTTGGTATAACCAACTAAAGCAGAGCTCACTATT
GATATCGTCATTTTATCCGACTAGCGCTGGGCACAACCTTCATCAGTTGAACTGACTAGTGATGG
GCACACAAATCGTCG
Found at i:3383 original size:21 final size:21
Alignment explanation
Indices: 3357--3432 Score: 118
Period size: 21 Copynumber: 3.6 Consensus size: 21
3347 ATAACTTCTT
*
3357 TGTCGCGACACAAGCAT-AGTG
1 TGTCGCGACACAAAC-TCAGTG
3378 TGTCGCGACACAAACTCAGTG
1 TGTCGCGACACAAACTCAGTG
*
3399 TGTCGCGACATAAACTCAGTG
1 TGTCGCGACACAAACTCAGTG
3420 TGTCGCGACACAA
1 TGTCGCGACACAA
3433 CATCGACTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (21 bp):
TGTCGCGACACAAACTCAGTG
Found at i:7519 original size:21 final size:21
Alignment explanation
Indices: 7475--7523 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
7465 TAGATGCATG
* *
7475 ACTTGTTTCGGTAGAAGTGAA
1 ACTTGTATCGGTAGAACTGAA
7496 ACTTGTATCGGTAGAACT-ATA
1 ACTTGTATCGGTAGAACTGA-A
7517 ACTTGTA
1 ACTTGTA
7524 CCGGCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACTGAA
Found at i:9292 original size:33 final size:33
Alignment explanation
Indices: 9216--9292 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
9206 CCTATTTACT
* * * * *
9216 TAAAATAAATAATTTTAGTCAAAATAAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
9249 GAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
9281 TAAAATAAACAA
1 TAAAATAAACAA
9293 CTTTGACTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:10091 original size:128 final size:128
Alignment explanation
Indices: 9863--10165 Score: 588
Period size: 128 Copynumber: 2.4 Consensus size: 128
9853 GACCTAATCA
*
9863 AATCTTTTTACGCGAATTGAGATGACAAGCAAAGCACCTCAACCCGGTTACTCAATTTGAAAAGT
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAAAAGT
9928 CGATAGCTTATATTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCAGTTCGTCACTCG
66 CGATAGCTTATATTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCAGTTCGTCACTCG
9991 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAAAAGT
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAAAAGT
*
10056 CGATAGCTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCAGTTCGTCACTCG
66 CGATAGCTTATATTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCAGTTCGTCACTCG
10119 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGG
1 AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGG
10166 CTCATTTAAA
Statistics
Matches: 173, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 173 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (128 bp):
AATCTTTTTACGCGAATTGAGATGACAAGCCAAGCACCTCAACCCGGTTACTCAATTTGAAAAGT
CGATAGCTTATATTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGCTTCAGTTCGTCACTCG
Found at i:14944 original size:15 final size:14
Alignment explanation
Indices: 14923--14957 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
14913 ATGAAAAATG
14923 AGAAAAAGGAAGAAAA
1 AGAAAAA-GAAG-AAA
14939 AGAAAAAGAAGAAA
1 AGAAAAAGAAGAAA
14953 AGAAA
1 AGAAA
14958 TTTATGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 4 0.21
16 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAGAAA
Found at i:17908 original size:192 final size:193
Alignment explanation
Indices: 17561--17919 Score: 596
Period size: 192 Copynumber: 1.9 Consensus size: 193
17551 TATAATCAAG
* *
17561 TTCCGACTAAAGTACAATGATTGAACTCCCTTTTATAAGTCTGTTACACTCATAGAATATATGAC
1 TTCCGACTAAAGTACAATGATTGAAATCCCTCTTATAAGTCTGTTACACTCATAGAATATATGAC
*
17626 TGCTTGTGGACGTACCAACGTCCAGAGTAATAATCCTGCACAAAATATATCAATTAGGCGATATC
66 TGCTTGTGGACGTACCAACGTCCAGAGTAATAATCCTGCACAAAATATATCAATTAGGCGATACC
* ** *
17691 CACAAGTATATGGGTAAGGTTGTAATATAGTTACAATTATAATATTATTTAATCATGGTGTCA
131 CACAAGGATACAGGTAAGATTGTAATATAGTTACAATTATAATATTATTTAATCATGGTGTCA
*
17754 TTCC-ACTAAAGTACAATGATTGAAATCCCTCTTATAAGTCTTTTACACTCATAGAATATATGAC
1 TTCCGACTAAAGTACAATGATTGAAATCCCTCTTATAAGTCTGTTACACTCATAGAATATATGAC
* *
17818 TGCCTT-TGGACTTACCAACGTCCAGAGTAATAATCCTGCACAAAATATATCAATTAGGTGATAC
66 TG-CTTGTGGACGTACCAACGTCCAGAGTAATAATCCTGCACAAAATATATCAATTAGGCGATAC
*
17882 CCATAAGGATACAGGTAAGATTGTAATATAGTTACAAT
130 CCACAAGGATACAGGTAAGATTGTAATATAGTTACAAT
17920 GAAGTAACGA
Statistics
Matches: 154, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
192 147 0.95
193 7 0.05
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (193 bp):
TTCCGACTAAAGTACAATGATTGAAATCCCTCTTATAAGTCTGTTACACTCATAGAATATATGAC
TGCTTGTGGACGTACCAACGTCCAGAGTAATAATCCTGCACAAAATATATCAATTAGGCGATACC
CACAAGGATACAGGTAAGATTGTAATATAGTTACAATTATAATATTATTTAATCATGGTGTCA
Found at i:20794 original size:13 final size:13
Alignment explanation
Indices: 20776--20802 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20766 GTTAAAGTTC
20776 TTTCACACATACA
1 TTTCACACATACA
20789 TTTCACACATACA
1 TTTCACACATACA
20802 T
1 T
20803 CCTTACAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (13 bp):
TTTCACACATACA
Found at i:30426 original size:96 final size:96
Alignment explanation
Indices: 30312--30503 Score: 330
Period size: 96 Copynumber: 2.0 Consensus size: 96
30302 AAAACTTAAA
*
30312 ACCCTAAATTAGAATAAAAAACTTTTAAACCCTAAGCCATAACCTCATAACTTATAACCATAAAT
1 ACCCTAAATTAGAATAAAAAACTTTTAAACCCTAAACCATAACCTCATAACTTATAACCATAAAT
*
30377 TCTAAACTCATAACCTCAAACCATTAAACCC
66 TCTAAACTCATAACCTCAAACCATCAAACCC
* * *
30408 ACCCTAAATTCGAATAAAAAACTTTTGAATCCTAAACCATAACCTCATAACTTATAACCATAAAT
1 ACCCTAAATTAGAATAAAAAACTTTTAAACCCTAAACCATAACCTCATAACTTATAACCATAAAT
*
30473 TCTAAACTCATAATCTCAAACCATCAAACCC
66 TCTAAACTCATAACCTCAAACCATCAAACCC
30504 TAAATCTAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.26
Consensus pattern (96 bp):
ACCCTAAATTAGAATAAAAAACTTTTAAACCCTAAACCATAACCTCATAACTTATAACCATAAAT
TCTAAACTCATAACCTCAAACCATCAAACCC
Found at i:30779 original size:9 final size:9
Alignment explanation
Indices: 30765--30789 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
30755 AATTAAAAAG
30765 TTAATTATT
1 TTAATTATT
30774 TTAATTATT
1 TTAATTATT
30783 TTAATTA
1 TTAATTA
30790 AAATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTAATTATT
Done.