Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011890.1 Kokia drynarioides strain JFW-HI SEQ_126887, 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: 59784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:281 original size:27 final size:27
Alignment explanation
Indices: 186--292 Score: 106
Period size: 27 Copynumber: 4.0 Consensus size: 27
176 CAATGTGGGG
* * *
186 TTGGTGCAGGCTGCCAGGTAGGCACCT
1 TTGGTGCCGCCTGTCAGGTAGGCACCT
* * * *
213 TTGGTGCCGCTTGGCAAGTAGGCACCA
1 TTGGTGCCGCCTGTCAGGTAGGCACCT
* * **
240 CTAGTGCCGGTTGTCAGGTAGGCACCT
1 TTGGTGCCGCCTGTCAGGTAGGCACCT
*
267 TTGGTGCCGCCTGTCAGATAGGCACC
1 TTGGTGCCGCCTGTCAGGTAGGCACC
293 ACCCCTTGTA
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.16, C:0.27, G:0.34, T:0.23
Consensus pattern (27 bp):
TTGGTGCCGCCTGTCAGGTAGGCACCT
Found at i:827 original size:19 final size:19
Alignment explanation
Indices: 799--877 Score: 99
Period size: 19 Copynumber: 4.3 Consensus size: 19
789 AACACATTTG
*
799 ATATTCACATCAATTTAAC
1 ATATTCACATCAATTTCAC
* * *
818 ATACTCACATCAATGTCAT
1 ATATTCACATCAATTTCAC
*
837 ATATTCACACCAATTTCAC
1 ATATTCACATCAATTTCAC
856 ATATTC-CAT-AATTTCAC
1 ATATTCACATCAATTTCAC
873 ATATT
1 ATATT
878 TTCATATCTC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 13 0.25
18 2 0.04
19 36 0.71
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (19 bp):
ATATTCACATCAATTTCAC
Found at i:1150 original size:45 final size:44
Alignment explanation
Indices: 1077--1205 Score: 125
Period size: 45 Copynumber: 2.9 Consensus size: 44
1067 ATGACTCACC
* * *
1077 ACCCCGGGTTGCCTGACAATGATGGCTCACTTATATTGAATTGCT
1 ACCCCGGGTTGCC-GACAAAGATAGCTCACTTATATCGAATTGCT
* **
1122 ACCCCGGGTTGCTCGGCAAAGATAGCTCAGC-TACGTCGAATTGCT
1 ACCCCGGGTTGC-CGACAAAGATAGCTCA-CTTATATCGAATTGCT
* * * *
1167 ACCCCAGGTTGCCCGATAACGATAGCTCACTTATGTCGA
1 ACCCCGGGTTG-CCGACAAAGATAGCTCACTTATATCGA
1206 TATGCAGTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
44 1 0.01
45 65 0.94
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (44 bp):
ACCCCGGGTTGCCGACAAAGATAGCTCACTTATATCGAATTGCT
Found at i:2262 original size:26 final size:26
Alignment explanation
Indices: 2231--2285 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 26
2221 CTTATAGCTA
2231 ACTTAATTAATAAAAATTAATTAACT
1 ACTTAATTAATAAAAATTAATTAACT
2257 AC----TTAATAAAAATTAATTAACT
1 ACTTAATTAATAAAAATTAATTAACT
2279 ACTTAAT
1 ACTTAAT
2286 AAAAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
22 22 0.88
26 3 0.12
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (26 bp):
ACTTAATTAATAAAAATTAATTAACT
Found at i:2263 original size:22 final size:22
Alignment explanation
Indices: 2237--2294 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
2227 GCTAACTTAA
2237 TTAATAAAAATTAATTAACTAC
1 TTAATAAAAATTAATTAACTAC
2259 TTAATAAAAATTAATTAACTAC
1 TTAATAAAAATTAATTAACTAC
2281 TTAATAAAAATTAA
1 TTAATAAAAATTAA
2295 GGTGTGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAATAAAAATTAATTAACTAC
Found at i:2881 original size:32 final size:32
Alignment explanation
Indices: 2833--2897 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2823 GATAGGCTTC
* *
2833 TCCAACAATTCGTTGAATCAGGTTAATTCATG
1 TCCAACAATTCATTGAATCAGGTCAATTCATG
* *
2865 TCCATCAATTCATTGAATCGGGTCAATTCATG
1 TCCAACAATTCATTGAATCAGGTCAATTCATG
2897 T
1 T
2898 GGATTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (32 bp):
TCCAACAATTCATTGAATCAGGTCAATTCATG
Found at i:18624 original size:21 final size:19
Alignment explanation
Indices: 18600--18642 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
18590 CATGCTTTTT
*
18600 AAAGGCTAAAAATTCAATTTA
1 AAAGACTAAAAA-TC-ATTTA
*
18621 AAAGACTAAATATCATTTA
1 AAAGACTAAAAATCATTTA
18640 AAA
1 AAA
18643 CTAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAGACTAAAAATCATTTA
Found at i:24398 original size:18 final size:18
Alignment explanation
Indices: 24364--24398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24354 TCCTCATTAT
*
24364 TAAAAATAATAGAGAATG
1 TAAAAATAAAAGAGAATG
*
24382 TAAAAATAAAAGTGAAT
1 TAAAAATAAAAGAGAAT
24399 AAATACTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (18 bp):
TAAAAATAAAAGAGAATG
Found at i:25040 original size:18 final size:18
Alignment explanation
Indices: 25019--25059 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
25009 TTCCATAAGA
*
25019 TCTTCCTCAGGGTCTTCT
1 TCTTCCTCAGGATCTTCT
25037 TCTTCCTCAGGATCTTCT
1 TCTTCCTCAGGATCTTCT
25055 TCTTC
1 TCTTC
25060 TCCTTCAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.34, G:0.12, T:0.46
Consensus pattern (18 bp):
TCTTCCTCAGGATCTTCT
Found at i:28046 original size:20 final size:22
Alignment explanation
Indices: 28021--28062 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
28011 AAAAAAAATT
28021 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
28041 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
28063 TCGTTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:28052 original size:29 final size:28
Alignment explanation
Indices: 27990--28059 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
27980 AATTACAATT
27990 ATTTAATAATTTTATTATTTCAAAAAAA
1 ATTTAATAATTTTATTATTTCAAAAAAA
*
28018 A-TTAATAATTTTA-TATTTTAAAAAATA
1 ATTTAATAATTTTATTATTTCAAAAAA-A
28045 ATTTTAATAATTTTA
1 A-TTTAATAATTTTA
28060 AAATCGTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 11 0.29
27 14 0.37
28 1 0.03
29 12 0.32
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTAATAATTTTATTATTTCAAAAAAA
Found at i:28368 original size:28 final size:30
Alignment explanation
Indices: 28318--28376 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
28308 ATGCCTTAAA
28318 AATATTTACAAAAAAAGACAACT-AATTTT
1 AATATTTACAAAAAAAGACAACTAAATTTT
**
28347 AATATTTACAAAATTA-ACAACTAAATTTT
1 AATATTTACAAAAAAAGACAACTAAATTTT
28376 A
1 A
28377 CAAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAAAGACAACTAAATTTT
Found at i:35799 original size:158 final size:158
Alignment explanation
Indices: 35511--35991 Score: 610
Period size: 158 Copynumber: 3.0 Consensus size: 158
35501 ATTTTGGGAT
* * * **
35511 TTACAGGTTATATGGGTGCTAGTCTTAGATGTCCTATCGATGGCTAAGATCCGGCATATGTTTGG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGGCATATGTTACG
* * * * * * *
35576 GATTCTACATAGCTCGTGTGACCAGCATCGTGTAGCCAAACATGTTGACCCACAGCTTGTATGAG
66 GATTCTCCATAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTTGACCTACAGCTCGTGTGAG
35641 TAGGCCCACTTTACAACTCGTGTGAGCA
131 TAGGCCCACTTTACAACTCGTGTGAGCA
* * *
35669 TTACATGTTATATGGGTGCTAGTCTTAAAGGTCCTACCGATGGCTGAGATCCGGTATATGTTACG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGGCATATGTTACG
* * *
35734 GATTCTCCATTA-CTTGTGTGAGCAGCATCGTGTGGCCTAACATCTTGACCTATAGCTCGTGTGA
66 GATTCTCCA-TAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTTGACCTACAGCTCGTGTGA
* *
35798 GTAGGCCCACTTTATAGCTCGTGTGAGCA
130 GTAGGCCCACTTTACAACTCGTGTGAGCA
* * * * *
35827 TTACATGTTATATGGTTCCTGGTCTTAGATGTCCTACCGATGGCTGAGATTCGGCATATGTTGCG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGGCATATGTTACG
* * *
35892 GATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCCTAACATCATGA-CTCACAGCTCGTGTGA
66 GATTCTCCATAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTTGACCT-ACAGCTCGTGTGA
* * *
35956 GCAGACCCA-TTT-CAGAGCTCGTATGAGCA
130 GTAGGCCCACTTTACA-A-CTCGTGTGAGCA
*
35985 CTACATG
1 TTACATG
35992 ATACAGAGAT
Statistics
Matches: 278, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
156 1 0.00
157 6 0.02
158 269 0.97
159 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (158 bp):
TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGGCATATGTTACG
GATTCTCCATAGCTCGTGTGAGCAGCATCGTGTAGCCTAACATCTTGACCTACAGCTCGTGTGAG
TAGGCCCACTTTACAACTCGTGTGAGCA
Done.