Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002985.1 Kokia drynarioides strain JFW-HI SEQ_115472, 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: 2153
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Found at i:1269 original size:208 final size:207
Alignment explanation
Indices: 894--1448 Score: 711
Period size: 208 Copynumber: 2.7 Consensus size: 207
884 AATGACAGTA
* *
894 ATCTTCCTGATGAGATATAGAGAAGTAGATCAAATCAATGAAGCGAAGCTCAATAT-GAATGAGA
1 ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAAT-TCGAATGAGA
* * * * **
958 CTTC--A----A-C--CTGATGCGATATAGAGAAGTGGGTCAAAGAAATAAAGTGACCATCTTCC
65 CTTCAAACCCCATCTTCTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCC
*
1014 TAATGAGATACAGAGAAGTGGATCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAAT
130 TAATGAGATACAGAGAAGTGGAGCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAAT
1079 -TAATGAAGAGGTC
195 CT-ATGAAGAGGTC
* *
1092 ATCTTCCTGATGAGATACATAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATTCGAATGAGAC
1 ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATTCGAATGAGAC
* *
1157 TTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATATTCC
66 TTCAAACCCCATCTTC-TGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCC
* * * *
1222 TGATGAGATACAGAGAAGTGGAGCAAATTTGCCTTCCTGATGAGATACAGAGAAGTGGATTGAAT
130 TAATGAGATACAGAGAAGTGGAGCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAAT
*
1287 CTATGAAGCGGTC
195 CTATGAAGAGGTC
* * ** * ** * *
1300 ATCCTT-CAGATGAGATACAGAGAAGTAAACTGAATAAATGAAATGAAGCTAAATACGAATGAGA
1 AT-CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATTCGAATGAGA
* * *
1364 TTTTAAACCCCATCTTCCTGATGAGATAAAGAGAAGTGGGCCAAAGCAATAAAGAGGTCATCTTC
65 CTTCAAACCCCATCTT-CTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTC
1429 CTAATGAGATACAGAGAAGT
129 CTAATGAGATACAGAGAAGT
1449 ACACAAAATC
Statistics
Matches: 309, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
197 1 0.00
198 62 0.20
200 1 0.00
204 1 0.00
205 1 0.00
207 1 0.00
208 237 0.77
209 5 0.02
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (207 bp):
ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATTCGAATGAGAC
TTCAAACCCCATCTTCTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCT
AATGAGATACAGAGAAGTGGAGCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAATC
TATGAAGAGGTC
Found at i:1317 original size:85 final size:85
Alignment explanation
Indices: 1169--1325 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
1159 CAAACCCCAT
* * *
1169 CTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATATTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCATATTCCAGATGAGATACA
1234 GAGAAGTGGAGCAAATTTGC
66 GAGAAGTGGAGCAAATTTGC
** * * * * *
1254 CTTCCTGATGAGATACAGAGAAGTGGATTGAATCTATGAAGCGGTCATCCTT-CAGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCAT-ATTCCAGATGAGATAC
1318 AGAGAAGT
65 AGAGAAGT
1326 AAACTGAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 59 0.97
86 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCATATTCCAGATGAGATACA
GAGAAGTGGAGCAAATTTGC
Found at i:1478 original size:123 final size:124
Alignment explanation
Indices: 1309--1572 Score: 289
Period size: 124 Copynumber: 2.1 Consensus size: 124
1299 CATCCTTCAG
** ** * * *
1309 ATGAGATACAGAGAAGTAAACTGAATAAATGAAATGAAGCTAAATACGAATGAGATTTTAAACCC
1 ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
* *
1374 C-ATCTTCCTGATGAGATAAAGAGAAGTGGGCCA-AAGCAATAAAGAGGTCATCTTCCTA
66 CTATCTTCCTGATGAGATAAAGAGAAGTGGG-CAGAAGCAATAAAGAGATCAGCTTCCTA
* * * * * *
1432 ATGAGATACAGAGAAGTACACAAAATCAATGAAGCAAAGTTCAATACGAGTGAAACTTCAAACCC
1 ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
* * * * * ** *
1497 CTATTTTCTTGATGAGATACAGAGAAGTGGGTAGAAGTAATAAATTGATCAGCTTCCTG
66 CTATCTTCCTGATGAGATAAAGAGAAGTGGGCAGAAGCAATAAAGAGATCAGCTTCCTA
*
1556 ATGAGATACAGGGAAGT
1 ATGAGATACAGAGAAGT
1573 GGACCAAGAG
Statistics
Matches: 115, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
123 54 0.47
124 61 0.53
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (124 bp):
ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
CTATCTTCCTGATGAGATAAAGAGAAGTGGGCAGAAGCAATAAAGAGATCAGCTTCCTA
Found at i:2087 original size:27 final size:27
Alignment explanation
Indices: 2056--2115 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2046 CCAAATTACA
* * *
2056 AAACCCAATACCACTAAGCC-AAACACT
1 AAACCCAAAACCACAAACCCTAAA-ACT
2083 AAACCCAAAACCACAAACCCTAAAACT
1 AAACCCAAAACCACAAACCCTAAAACT
2110 AAACCC
1 AAACCC
2116 TGACCCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.52, C:0.38, G:0.02, T:0.08
Consensus pattern (27 bp):
AAACCCAAAACCACAAACCCTAAAACT
Done.