Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012566.1 Kokia drynarioides strain JFW-HI SEQ_127575, 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: 15642
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:449 original size:22 final size:22
Alignment explanation
Indices: 414--457 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
404 TTCATCTTGA
414 CTTTCCTTTCTTCTCTTTCTTTT
1 CTTTCCTTTCTTCTCTTT-TTTT
*
437 CTTT-CTTTTTTCTCTTTTTTT
1 CTTTCCTTTCTTCTCTTTTTTT
458 ATCGGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
CTTTCCTTTCTTCTCTTTTTTT
Found at i:5047 original size:201 final size:200
Alignment explanation
Indices: 4561--5161 Score: 835
Period size: 201 Copynumber: 3.0 Consensus size: 200
4551 ATTTGGTCCA
** * * * * * * *
4561 CATCACTTGTTTTGATCCACTTCTCTATGTTTCATCAGGAAAACGGATTTGGTTCACTTCTCAAT
1 CATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAAT
* *
4626 ATCTCATCAGGAAGCTAACCGTTTTATTGCTTCGACCCGCTTCTCAGTATCTTATCAGGAAGCTG
66 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTG
* * * * *
4691 AGATTCGAAGATTTGCTCACATCGAGCATGGGTTTG-ATTAGGCCTTCTTCTCAGTATCTCATCA
131 GGGTTCGAAGATTTGCTCACATCGAGCCTGAGTTGGTA-TA---CTTC-TCT--GTATCTCATCA
*
4755 GGAGGATGACCG
189 GGAAGATGACCG
** *
4767 CATTGCTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGT
1 CATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAAT
*
4832 ATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTG
66 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTG
* *
4897 GGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGA
131 GGGTTCGAAGATTTGCTCACATCGAGCCT-GAGTTGGTATACTTCTCTGTATCTCATCAGGAAGA
4962 TGACCG
195 TGACCG
* ** *
4968 CCTCACTTGTTTCAATTTGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAAT
1 CATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAAT
* *
5033 GTCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG
66 ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTG
* *
5098 GTGTTCGAAGATTTGCTCACATCGAGCGCTGAGTTGGTATACTTCTCTGTATCTCATTAGGAAG
131 GGGTTCGAAGATTTGCTCACATCGAGC-CTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAG
5162 CTGGGGCTCA
Statistics
Matches: 355, Mismatches: 37, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
201 199 0.56
202 2 0.01
203 3 0.01
204 4 0.01
206 139 0.39
207 7 0.02
208 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (200 bp):
CATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAAT
ATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTG
GGGTTCGAAGATTTGCTCACATCGAGCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGAT
GACCG
Found at i:5180 original size:67 final size:67
Alignment explanation
Indices: 5072--5228 Score: 217
Period size: 67 Copynumber: 2.3 Consensus size: 67
5062 CTTCGACCTG
* * * *
5072 CTTCTCAGTATCTCATCAGGAAGCTGGTGTTCGAAGATTTGCTCACATCGAGCGCT-GAGTTGGT
1 CTTCTCTGTATCTCATCAGGAAGCTGGGGCTCAAAGATTTGCTCACATCGAGC-CTCGAGTTGGT
5136 ATA
65 ATA
* * * * *
5139 CTTCTCTGTATCTCATTAGGAAGCTGGGGCTCAAAGATTTGCTCGCATTGAGCTTCGAGTTGGTT
1 CTTCTCTGTATCTCATCAGGAAGCTGGGGCTCAAAGATTTGCTCACATCGAGCCTCGAGTTGGTA
5204 TA
66 TA
5206 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
5229 ATGACCGCCT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
66 1 0.01
67 78 0.99
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (67 bp):
CTTCTCTGTATCTCATCAGGAAGCTGGGGCTCAAAGATTTGCTCACATCGAGCCTCGAGTTGGTA
TA
Found at i:5374 original size:268 final size:268
Alignment explanation
Indices: 4871--5428 Score: 911
Period size: 268 Copynumber: 2.1 Consensus size: 268
4861 CTTCGACCTG
* * * *
4871 CTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTCGAGTTGGTA
1 CTTCTCTGTATCTCATCAGGAAGCTGGGGCTCAAAGATTTGCTCGCATTGAGCCTCGAGTTGGTA
*
4936 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTTGCTTCTCTGTATCTC
66 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTC
* * * * *
5001 ATCAGGAAGACAAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACCATTTTATTGCTTC
131 ATCAGGAAAACAAATTTGATCCACTTCTCAATATCTCATAAGGAAGCTAACAATTTTATTGCTTC
* *
5066 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGTGTTCGAAGATTTGCTCACATCGAGCGCTGAG
196 GACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGCTGAG
5131 TTGGTATA
261 TTGGTATA
* * *
5139 CTTCTCTGTATCTCATTAGGAAGCTGGGGCTCAAAGATTTGCTCGCATTGAGCTTCGAGTTGGTT
1 CTTCTCTGTATCTCATCAGGAAGCTGGGGCTCAAAGATTTGCTCGCATTGAGCCTCGAGTTGGTA
*
5204 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTTTGTATCTC
66 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTC
* * * *
5269 ATCAGGAAAACGAATTTGATCCACTTCTCAGTATCTCATAAGGACGCTAACAATTTTATTGCTTT
131 ATCAGGAAAACAAATTTGATCCACTTCTCAATATCTCATAAGGAAGCTAACAATTTTATTGCTTC
* *
5334 GACCTACTTCTCAGTATCTCATCAGGACGCTGGGGTTCGAAGATTTGCTCACATCGAGCGCTGGG
196 GACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGCTGAG
5399 TTGGTATA
261 TTGGTATA
5407 CTTCTCTG-ATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
5429 ATAACCGCCT
Statistics
Matches: 267, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
267 13 0.05
268 254 0.95
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (268 bp):
CTTCTCTGTATCTCATCAGGAAGCTGGGGCTCAAAGATTTGCTCGCATTGAGCCTCGAGTTGGTA
TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTC
ATCAGGAAAACAAATTTGATCCACTTCTCAATATCTCATAAGGAAGCTAACAATTTTATTGCTTC
GACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGCTGAG
TTGGTATA
Found at i:12451 original size:23 final size:22
Alignment explanation
Indices: 12421--12463 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
12411 AATTTTTTTA
12421 AAAAAAAAGGGAAAAGAGAAGTT
1 AAAAAAAA-GGAAAAGAGAAGTT
12444 AAAAAAAAGGAAAAGAGAAG
1 AAAAAAAAGGAAAAGAGAAG
12464 GTTTTTGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.05
Consensus pattern (22 bp):
AAAAAAAAGGAAAAGAGAAGTT
Found at i:13257 original size:30 final size:29
Alignment explanation
Indices: 13198--13420 Score: 202
Period size: 29 Copynumber: 7.6 Consensus size: 29
13188 CCCTAATCTG
* * *
13198 TCCAAAAATTCTATTTTTACCTTTGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
*
13227 TCCAAAAATTCCATTTTTGA-CCTTGAAACT
1 TCCAAAAATTCCATTTTT-ACCCTCG-AACT
* * *
13257 TCAAAAAATTCCATTTTCACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACT
*
13286 TCCAAAAATTCTATTTTTGA-CCTCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCTCG-AACT
* *
13316 TCCAAAAATTTCATTTTTACCCTCGAACC
1 TCCAAAAATTCCATTTTTACCCTCGAACT
* * *
13345 TCCAAAATTTCCATTTTTATCATCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCG-AACT
* * *
13375 TTCAAAAATTACCA-TTTTGCCCTCGGA-T
1 TCCAAAAATT-CCATTTTTACCCTCGAACT
*
13403 GTCCAAAAACTCCATTTT
1 -TCCAAAAATTCCATTTT
13421 CGATCTCGAA
Statistics
Matches: 158, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.03
29 82 0.52
30 69 0.44
31 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCTCGAACT
Found at i:13291 original size:59 final size:58
Alignment explanation
Indices: 13222--13433 Score: 223
Period size: 59 Copynumber: 3.6 Consensus size: 58
13212 TTTTACCTTT
*
13222 GAACTTCCAAAAATTCCATTTTTGACCTTGAAACTTCAAAAAATTCCATTTTCACCCCC
1 GAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC-AAAAATTCCATTTTCACCCCC
* * * *
13281 GAACTTCCAAAAATTCTATTTTTGACCTCGAAACTTCCAAAAATTTCATTTTTACCCTC
1 GAACTTCCAAAAATTCCATTTTTGACCTCGAAACTT-CAAAAATTCCATTTTCACCCCC
* * * * *
13340 GAACCTCCAAAATTTCCATTTTT-ATCATCGAAACTTTCAAAAATTACCATTTT-GCCCTC
1 GAACTTCCAAAAATTCCATTTTTGA-CCTCGAAAC-TTCAAAAATT-CCATTTTCACCCCC
* * * *
13399 GGA-TGTCCAAAAACTCCATTTTCGATCTCGAAACT
1 GAACT-TCCAAAAATTCCATTTTTGACCTCGAAACT
13434 CTCGAAATTA
Statistics
Matches: 129, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.02
59 117 0.91
60 10 0.08
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.34
Consensus pattern (58 bp):
GAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCAAAAATTCCATTTTCACCCCC
Found at i:13834 original size:96 final size:96
Alignment explanation
Indices: 13728--13919 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 96
13718 AAAACTTTAA
* **
13728 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCAAAAATTTGTGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-AAAAATTTACGCCTTAACTTACTAGGTGCA
**
13790 ATTTTTCTTCAAATCGAA-ATAATCGAATACCCTT
63 ACCTTTCTTCAAATC-AAGATAATCGAATACCCTT
*
13824 AATCGAGGCAATGTTTCCTTATCTTCGATTCTAAAAATTTACGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTAAAAATTTACGCCTTAACTTACTAGGTGCAACC
*
13889 TTTCTTCAAATCAAGATAATCGAATATCCTT
66 TTTCTTCAAATCAAGATAATCGAATACCCTT
13920 TTCTAATAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
95 2 0.02
96 74 0.87
97 9 0.11
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTAAAAATTTACGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAGATAATCGAATACCCTT
Done.