Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004553.1 Kokia drynarioides strain JFW-HI SEQ_118025, 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: 61656
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:441 original size:14 final size:14
Alignment explanation
Indices: 422--457 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
412 GAAAAGCAAT
*
422 TCATTTTCTAGAAA
1 TCATTTTCCAGAAA
436 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
450 TCATTTTC
1 TCATTTTC
458 AGTCAAACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:9797 original size:14 final size:14
Alignment explanation
Indices: 9778--9808 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9768 CAATGTTAAA
*
9778 TTTTATTTTTATTG
1 TTTTATTTTTAATG
9792 TTTTATTTTTAATG
1 TTTTATTTTTAATG
9806 TTT
1 TTT
9809 GTTTGGCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTAATG
Found at i:12174 original size:14 final size:14
Alignment explanation
Indices: 12157--12193 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12147 TTTCTTTATC
12157 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
* *
12171 TTTTTTGTTTTGAA
1 TTTTTTTTTTTCAA
12185 TTTTTTTTT
1 TTTTTTTTT
12194 CTTTTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTTCAA
Found at i:15345 original size:21 final size:21
Alignment explanation
Indices: 15294--15345 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
15284 AACCTATCAG
*
15294 AAACAAATAAAAGGAAAAAATT
1 AAACAAA-AAAAGGAAAAAATA
** * *
15316 AAATTAAAAATGGAAACAATA
1 AAACAAAAAAAGGAAAAAATA
15337 AAACAAAAA
1 AAACAAAAA
15346 TAAAAAAATG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (21 bp):
AAACAAAAAAAGGAAAAAATA
Found at i:16248 original size:158 final size:158
Alignment explanation
Indices: 15960--16275 Score: 623
Period size: 158 Copynumber: 2.0 Consensus size: 158
15950 GCTAGATCTA
15960 CTCTTAAACAGGGTTGATAGTATTAGAAAAAACCATTGATTTCTTCCTACTTTTTGTTTAAGTTG
1 CTCTTAAACAGGGTTGATAGTATTAGAAAAAACCATTGATTTCTTCCTACTTTTTGTTTAAGTTG
16025 TTCCCATTTGGTCATCCTTAGTATATATTTTTAGCATTTTTTAATTTAGTTATTGCATTTTCTAA
66 TTCCCATTTGGTCATCCTTAGTATATATTTTTAGCATTTTTTAATTTAGTTATTGCATTTTCTAA
16090 CTTAATAGAACTTAGCTTAATTGCCCTT
131 CTTAATAGAACTTAGCTTAATTGCCCTT
16118 CTCTTAAACAGGGTTGATAGTATTAGAAAAAACCATTGATTTCTTCCTACTTTTTGTTTAAGTTG
1 CTCTTAAACAGGGTTGATAGTATTAGAAAAAACCATTGATTTCTTCCTACTTTTTGTTTAAGTTG
16183 TTCCCATTTGGTCATCCTTAGTATATATTTTTAGCATTTTTTAATTTAGTTATTGCATTTTCTAA
66 TTCCCATTTGGTCATCCTTAGTATATATTTTTAGCATTTTTTAATTTAGTTATTGCATTTTCTAA
*
16248 CTTAATGGAACTTAGCTTAATTGCCCTT
131 CTTAATAGAACTTAGCTTAATTGCCCTT
16276 GATTTTATAA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 157 1.00
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.46
Consensus pattern (158 bp):
CTCTTAAACAGGGTTGATAGTATTAGAAAAAACCATTGATTTCTTCCTACTTTTTGTTTAAGTTG
TTCCCATTTGGTCATCCTTAGTATATATTTTTAGCATTTTTTAATTTAGTTATTGCATTTTCTAA
CTTAATAGAACTTAGCTTAATTGCCCTT
Found at i:41669 original size:22 final size:22
Alignment explanation
Indices: 41641--41682 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
41631 GCAGTCACTG
41641 CCACTAGAAGCTATAGTGACTA
1 CCACTAGAAGCTATAGTGACTA
*
41663 CCACTAGAAGCTGTAGTGAC
1 CCACTAGAAGCTATAGTGAC
41683 AATTTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.21
Consensus pattern (22 bp):
CCACTAGAAGCTATAGTGACTA
Found at i:54172 original size:18 final size:18
Alignment explanation
Indices: 54151--54196 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
54141 AGCTTGTGGT
54151 TGCATCTGGTTATATGAA
1 TGCATCTGGTTATATGAA
* * * *
54169 TGCATCTGATTTTGTGAT
1 TGCATCTGGTTATATGAA
54187 TGCATCTGGT
1 TGCATCTGGT
54197 CATGTAATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43
Consensus pattern (18 bp):
TGCATCTGGTTATATGAA
Found at i:58215 original size:194 final size:194
Alignment explanation
Indices: 57873--58255 Score: 599
Period size: 194 Copynumber: 2.0 Consensus size: 194
57863 TTTCCTCCTA
* * * *
57873 GATATGGCCTTAGTCAGCAATAGTTTTGAACCTCATAGTCCACGATATTAAATTTTATTTTTACT
1 GATATGGCCTTAGTCAACAATAGTTTTAAACCTCAAAGTCCACGATATTAAATTTTATATTTACT
*
57938 GTTATATTTTCTACATTTGTTTGGCAAGTCAATCTCGAGAGTCCTCAAGGCAAACATGAACATGT
66 GTTATATTTTCTACATTTGTTTGGAAAGTCAATCTCGAGAGTCCTCAAGGCAAACATGAACATGT
* *
58003 TCATGCAGCCAGCAAACATATGGTATACGGTCTCTATTGTAGCATTCATGAGCCTTGATCCTTT
131 TCATGCACCCAACAAACATATGGTATACGGTCTCTATTGTAGCATTCATGAGCCTTGATCCTTT
*
58067 GATATGGCCTTAGTCAACAATAGTTTTAAACCTCAAAGTCCACGATATTAAATTTTATATTTATT
1 GATATGGCCTTAGTCAACAATAGTTTTAAACCTCAAAGTCCACGATATTAAATTTTATATTTACT
* * *
58132 GTTATATTTTCTACGTTTGTTT-GAAATGGT-AATCTTGAGAGTCCTCAAGGCAAACATGAAGAT
66 GTTATATTTTCTACATTTGTTTGGAAA--GTCAATCTCGAGAGTCCTCAAGGCAAACATGAACAT
* * * *
58195 GTTCATGTACCCAACAAACATATGGTATACTGTCTCTGTTGTAGCATTCCTGAGCCTTGAT
129 GTTCATGCACCCAACAAACATATGGTATACGGTCTCTATTGTAGCATTCATGAGCCTTGAT
58256 TCATTGAAGT
Statistics
Matches: 172, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
193 3 0.02
194 167 0.97
195 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (194 bp):
GATATGGCCTTAGTCAACAATAGTTTTAAACCTCAAAGTCCACGATATTAAATTTTATATTTACT
GTTATATTTTCTACATTTGTTTGGAAAGTCAATCTCGAGAGTCCTCAAGGCAAACATGAACATGT
TCATGCACCCAACAAACATATGGTATACGGTCTCTATTGTAGCATTCATGAGCCTTGATCCTTT
Done.