Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002303.1 Kokia drynarioides strain JFW-HI SEQ_114341, 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: 4800
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Found at i:730 original size:15 final size:16
Alignment explanation
Indices: 710--739 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
700 AAAATTTTAG
710 ATTTTTTCT-AAAAAT
1 ATTTTTTCTCAAAAAT
725 ATTTTTTCTCAAAAA
1 ATTTTTTCTCAAAAA
740 CACTTTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTTTCTCAAAAAT
Found at i:1182 original size:18 final size:19
Alignment explanation
Indices: 1159--1195 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1149 AATATTTTTC
*
1159 TCATAAAAATATTA-AAAA
1 TCATAAAAACATTATAAAA
1177 TCATAAAAACATTATAAAA
1 TCATAAAAACATTATAAAA
1196 ATTAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
TCATAAAAACATTATAAAA
Found at i:1237 original size:16 final size:15
Alignment explanation
Indices: 1214--1262 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1204 AATTTTATAA
1214 AAATATTTAAATTGAT
1 AAATATTTAAATT-AT
*
1230 ATATATTTAAATTAT
1 AAATATTTAAATTAT
*
1245 AAATATTATAAAATAT
1 AAATATT-TAAATTAT
1261 AA
1 AA
1263 TAACTTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
AAATATTTAAATTAT
Found at i:1381 original size:18 final size:19
Alignment explanation
Indices: 1354--1407 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1344 CTTAAAAATA
*
1354 ATAAATAATTATAAAAAGTT
1 ATAAA-AATTATAAAAACTT
* *
1374 -TTAAAATTATATAAACTT
1 ATAAAAATTATAAAAACTT
1392 ATAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
1408 AATCATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAAAATTATAAAAACTT
Found at i:1388 original size:10 final size:9
Alignment explanation
Indices: 1346--1407 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
1336 GTAGAATTCT
*
1346 TAAAAATAA
1 TAAAAATTA
1355 TAAATAATTA
1 TAAA-AATTA
1365 TAAAAAGTT-
1 TAAAAA-TTA
*
1374 TTAAAATTA
1 TAAAAATTA
*
1383 TATAAACTTA
1 TA-AAAATTA
1393 TAAAAATTA
1 TAAAAATTA
1402 TAAAAA
1 TAAAAA
1408 AATCATAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 2 0.05
9 24 0.55
10 18 0.41
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1408 original size:10 final size:10
Alignment explanation
Indices: 1347--1418 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 10
1337 TAGAATTCTT
*
1347 AAAAATAATA
1 AAAAATTATA
*
1357 AATAATTATA
1 AAAAATTATA
*
1367 AAAAGTT-T-
1 AAAAATTATA
*
1375 TAAAATTATA
1 AAAAATTATA
* *
1385 TAAACTTAT-
1 AAAAATTATA
1394 AAAAATTATAA
1 AAAAATTAT-A
*
1405 AAAAATCATA
1 AAAAATTATA
1415 AAAA
1 AAAA
1419 CTTAAACTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
8 5 0.10
9 9 0.19
10 26 0.54
11 8 0.17
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1415 original size:28 final size:28
Alignment explanation
Indices: 1362--1416 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1352 TAATAAATAA
* **
1362 TTATAAAAAGTTTTAAAATTATATAAAC
1 TTATAAAAAGTTATAAAAAAATATAAAC
1390 TTATAAAAA-TTATAAAAAAATCATAAA
1 TTATAAAAAGTTATAAAAAAAT-ATAAA
1417 AACTTAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (28 bp):
TTATAAAAAGTTATAAAAAAATATAAAC
Done.