Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002986.1 Kokia drynarioides strain JFW-HI SEQ_115473, 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: 2163
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Found at i:1252 original size:208 final size:208
Alignment explanation
Indices: 894--1458 Score: 785
Period size: 208 Copynumber: 2.7 Consensus size: 208
884 GATGACAGTA
* *
894 ATCTTCCTGATGAGATATAGAGAAGTAGATCAAATCAATGAAGCGAAGCTCAATAT-GAATGAGA
1 ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAAT-TCGAATGAGA
* * * * * * **
958 CTTCAAACCCCATATTCCTGATGCGATATAGAAAAGTGGGTCAAAGAAATAAAGTGACCATCTTC
65 CTTCAAACCCCATCTTCCTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTC
*
1023 CTAATGAGATACAGAGAAGTGGATCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAA
130 CTAATGAGATACAGAGAAGTGGAGCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAA
1088 T-TAATGAAGAGGTC
195 TCT-ATGAAGAGGTC
* *
1102 ATCTTCCTGATGAGATACATAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATTCGAATGAGAC
1 ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATTCGAATGAGAC
* * *
1167 TTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATATTCC
66 TTCAAACCCCATCTTCCTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCC
* * * *
1232 TGATGAGATACAGAGAAGTGGAGCAAATTTGCCTTCCTGATGAGATACAGAGAAGTGGATTGAAT
131 TAATGAGATACAGAGAAGTGGAGCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAAT
*
1297 CTATGAAGCGGTC
196 CTATGAAGAGGTC
* * ** * ** * *
1310 ATCCTT-CAGATGAGATACAGAGAAGTAAACTGAATAAATGAAATGAAGCTAAATACGAATGAGA
1 AT-CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATTCGAATGAGA
* * *
1374 TTTTAAACCCCATCTTCCTGATGAGATAAAGAGAAGTGGGCCAAAGCAATAAAGAGGTCATCTTC
65 CTTCAAACCCCATCTTCCTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTC
1439 CTAATGAGATACAGAGAAGT
130 CTAATGAGATACAGAGAAGT
1459 ACACAAAATC
Statistics
Matches: 316, Mismatches: 38, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
207 1 0.00
208 311 0.98
209 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (208 bp):
ATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATTCGAATGAGAC
TTCAAACCCCATCTTCCTGATGAGATAAAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCC
TAATGAGATACAGAGAAGTGGAGCAAATCTGCCTTCCTGATGAGATACAGAGAAGTGAATTAAAT
CTATGAAGAGGTC
Found at i:1327 original size:85 final size:85
Alignment explanation
Indices: 1179--1335 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
1169 CAAACCCCAT
* * *
1179 CTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATATTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCATATTCCAGATGAGATACA
1244 GAGAAGTGGAGCAAATTTGC
66 GAGAAGTGGAGCAAATTTGC
** * * * * *
1264 CTTCCTGATGAGATACAGAGAAGTGGATTGAATCTATGAAGCGGTCATCCTT-CAGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCAT-ATTCCAGATGAGATAC
1328 AGAGAAGT
65 AGAGAAGT
1336 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:1488 original size:123 final size:124
Alignment explanation
Indices: 1319--1582 Score: 298
Period size: 124 Copynumber: 2.1 Consensus size: 124
1309 CATCCTTCAG
** ** * * *
1319 ATGAGATACAGAGAAGTAAACTGAATAAATGAAATGAAGCTAAATACGAATGAGATTTTAAACCC
1 ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
*
1384 C-ATCTTCCTGATGAGATAAAGAGAAGTGGGCCA-AAGCAATAAAGAGGTCATCTTCCTA
66 CTATCTTCCTGATGAGATAAAGAGAAGTGGG-CAGAAGCAATAAAGAGATCATCTTCCTA
* * * * * *
1442 ATGAGATACAGAGAAGTACACAAAATCAATGAAGCAAAGTTCAATACGAGTGAAACTTCAAACCC
1 ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
* * * * * ** *
1507 CTATTTTCTTGATGAGATACAGAGAAGTGGGTAGAAGTAATAAATTGATCATCTTCCTG
66 CTATCTTCCTGATGAGATAAAGAGAAGTGGGCAGAAGCAATAAAGAGATCATCTTCCTA
*
1566 ATGAGATACAGGGAAGT
1 ATGAGATACAGAGAAGT
1583 GGACCAAGAG
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
123 54 0.47
124 62 0.53
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (124 bp):
ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
CTATCTTCCTGATGAGATAAAGAGAAGTGGGCAGAAGCAATAAAGAGATCATCTTCCTA
Found at i:2097 original size:27 final size:27
Alignment explanation
Indices: 2066--2125 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2056 CCAAATTACA
* * *
2066 AAACCCAATACCACTAAGCC-AAACACT
1 AAACCCAAAACCACAAACCCTAAA-ACT
2093 AAACCCAAAACCACAAACCCTAAAACT
1 AAACCCAAAACCACAAACCCTAAAACT
2120 AAACCC
1 AAACCC
2126 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.