Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011213.1 Kokia drynarioides strain JFW-HI SEQ_126191, 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: 5994
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:450 original size:3 final size:3
Alignment explanation
Indices: 442--509 Score: 93
Period size: 3 Copynumber: 22.3 Consensus size: 3
432 CCTTTCGATT
*
442 TTA TTA TTA TTA TTA ATA TCTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
488 -TA TTA TTA TTA ATA TTAA TTA T
1 TTA TTA TTA TTA TTA TT-A TTA T
510 AGTTGCCATT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1205 original size:13 final size:13
Alignment explanation
Indices: 1187--1212 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1177 TCAGGCTTGA
1187 TTTGTAATTGGAC
1 TTTGTAATTGGAC
1200 TTTGTAATTGGAC
1 TTTGTAATTGGAC
1213 ATTATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:1237 original size:16 final size:17
Alignment explanation
Indices: 1229--1291 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
1219 TAAATAAATT
*
1229 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
1246 TAAA-TTAAATTTCAAA
1 TAAATTTAAATTTAAAA
* *
1262 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
1279 TAAATTCAAATTT
1 TAAATTTAAATTT
1292 TGTTGGGCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 14 0.37
17 24 0.63
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1251 original size:23 final size:22
Alignment explanation
Indices: 1216--1262 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1206 ATTGGACATT
1216 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAA-TTAAATTTCAA
1238 ATTTATAATAAATTAAATTTCAA
1 ATTTA-AATAAATTAAATTTCAA
1261 AT
1 AT
1263 AAACTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAAATAAATTAAATTTCAA
Found at i:2084 original size:200 final size:202
Alignment explanation
Indices: 1615--2094 Score: 516
Period size: 206 Copynumber: 2.4 Consensus size: 202
1605 TGACTTGGCC
* * * * ** * * *
1615 TTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTTTTTTGATCCACTTCTCTGTGTTTC
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCGCTTCTCTGTATCTC
* * ** * * ** * **
1680 ATCAGGAAGATGGTTTTGGTTCACTTCCTCGTATTTTGTCAGGAAGCTAACCATTTTATTACTTC
66 ATCAAGAAGACGAATTTGGTCCACTTCTTAATATCTCATCAGGAAGCTAACCATTTTATTACTTC
* * ** * *
1745 ATCCTACTTCTCAGTATCTTATCAAGAATTTGGGGTTCGAGGATTTGCTCACATCGAGCGCGGGT
131 ACCCTACTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGC--G-
** *
1810 TTGATTTGGTC
193 -TGAGATGGTA
* * * *
1821 TTCTTCTCAGTATCTCATCAGGAAGATGGCCGCATTGCTTGTTTCAATTCGCTTCTCTGTATCTC
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCGCTTCTCTGTATCTC
* *
1886 ATCAAGAAGACGAATTTGGTCCACTTCTTAATATCTCATCAGGAAGCTAACC-TTTTGTTGCTTC
66 ATCAAGAAGACGAATTTGGTCCACTTCTTAATATCTCATCAGGAAGCTAACCATTTTATTACTTC
* *
1950 GCCCTGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGTC-C-TG
131 ACCCTACTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAG-CGCGTG
2013 AGATGGTA
195 AGATGGTA
** * *
2021 TTCTTCTTTGTATCTCATCAGGAAGATGACCACCTTACTTGTTTCAATCCGCTTCTGTGTATCTC
1 TTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCGCTTCTCTGTATCTC
*
2086 ATCAGGAAG
66 ATCAAGAAG
2095 CTGGGATTCG
Statistics
Matches: 227, Mismatches: 46, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
200 72 0.32
205 61 0.27
206 94 0.41
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (202 bp):
TTCTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTCAATCCGCTTCTCTGTATCTC
ATCAAGAAGACGAATTTGGTCCACTTCTTAATATCTCATCAGGAAGCTAACCATTTTATTACTTC
ACCCTACTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGCGTGA
GATGGTA
Found at i:2111 original size:116 final size:114
Alignment explanation
Indices: 1952--2229 Score: 387
Period size: 116 Copynumber: 2.4 Consensus size: 114
1942 GTTGCTTCGC
* *
1952 CCTGCTTCTCAGTATCTCATCAAGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGTCCTGAGAT
1 CCTGCTTCTCAGTATCTCATCAGGAAGCTG-GGTTCGAAGATTTGCTCACATCGAGCCCTGAGAT
* * * *
2017 GGTATTCTTCTTTGTATCTCATCAGGAAGATGACCACCTTACTTGTTTCAA
65 GGTATACTTCTCTGTATCTCATCAGGAAGATAACCACCTTA-TTATTTCAA
** *
2068 TCC-GCTTCTGTGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGATCACATCGAGCCCTGAGA
1 -CCTGCTTCTCAGTATCTCATCAGGAAGCTGGG-TTCGAAGATTTGCTCACATCGAGCCCTGAGA
* ** *
2132 TGGTATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGA
64 TGGTATACTTCTCTGTATCTCATCAGGAAGATAACCACCTTATTATTTCAA
2183 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCT
1 CCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCT
2230 TGAGCGTTGG
Statistics
Matches: 142, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
114 2 0.01
115 46 0.32
116 92 0.65
117 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (114 bp):
CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGATG
GTATACTTCTCTGTATCTCATCAGGAAGATAACCACCTTATTATTTCAA
Found at i:2496 original size:200 final size:201
Alignment explanation
Indices: 2138--2613 Score: 740
Period size: 200 Copynumber: 2.4 Consensus size: 201
2128 GAGATGGTAT
*
2138 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
* * * *
2203 CAGGAAGCTGGGGTTCGAAGATTTGCTTGAGCGTTGGTTTGATTTGGCCTTCTTCTCAATATCTC
66 CAGGAAGCTGAGATTCGAAGATTTGCTCGAGCGTGGGTTTGATTTGGCCTTCTTCTCAATATCTC
* *
2268 GTCAGGAAGATGACCACGTCACTTGTTTCAATTCGCTTCTCTGTATCTTATCAAGAAGACGAATT
131 GTCAGGAAGATAACCACGTCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATT
2333 TAGTCC
196 TAGTCC
* * *
2339 ACTTCTCAT-TATCTCATCAAGAAGCTAACC-TTTTATTGCTTCGCCCTGCTTCTCAGTATCTCA
1 ACTTCTC-TGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* *
2402 TCAGGAAGCTGAGATTTGAAGATTTGCTCGAGCGTGGGTTTGATTTGGCCTTCTTCTCAGTATCT
65 TCAGGAAGCTGAGATTCGAAGATTTGCTCGAGCGTGGGTTTGATTTGGCCTTCTTCTCAATATCT
* * ** * *
2467 CGTTAGGAAGATAACCGCGTCGTTTGTTTCAATTCNCTTCTCTGTATCTCATCAGGAAGACGAAT
130 CGTCAGGAAGATAACCACGTCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAAT
*
2532 TTGGTCC
195 TTAGTCC
* *
2539 ACTGCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
2604 CAGGAAGCTG
66 CAGGAAGCTG
2614 GAGTTCACGG
Statistics
Matches: 248, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
199 1 0.00
200 178 0.72
201 68 0.27
202 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (201 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
CAGGAAGCTGAGATTCGAAGATTTGCTCGAGCGTGGGTTTGATTTGGCCTTCTTCTCAATATCTC
GTCAGGAAGATAACCACGTCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAGACGAATT
TAGTCC
Done.