Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006612.1 Kokia drynarioides strain JFW-HI SEQ_121202, 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, 882
Length: 1470
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Found at i:510 original size:11 final size:11
Alignment explanation
Indices: 496--530 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
486 CTTTTAATAA
496 TTTTTTGAATT
1 TTTTTTGAATT
*
507 TTTTTTGCATT
1 TTTTTTGAATT
*
518 TTTTTTAAATT
1 TTTTTTGAATT
529 TT
1 TT
531 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTTGAATT
Found at i:737 original size:13 final size:13
Alignment explanation
Indices: 699--740 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
689 ATTAACTACC
699 AATTAAATTAAAA
1 AATTAAATTAAAA
* *
712 AATTTACA-CAAAA
1 AA-TTAAATTAAAA
725 AATTAAATTAAAA
1 AATTAAATTAAAA
738 AAT
1 AAT
741 AATCATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAATTAAAA
Found at i:1155 original size:10 final size:10
Alignment explanation
Indices: 1140--1260 Score: 55
Period size: 10 Copynumber: 12.7 Consensus size: 10
1130 TGGCATGTGG
1140 TAAAAAATTA
1 TAAAAAATTA
1150 TAAAAAA--A
1 TAAAAAATTA
* *
1158 -AATAATATCA
1 TAA-AAAATTA
1168 ATAAA-AATTA
1 -TAAAAAATTA
1178 T-AAAAATTA
1 TAAAAAATTA
* *
1187 T-TAAATTTAA
1 TAAAAAATT-A
1197 TAAAAAATTA
1 TAAAAAATTA
1207 TAAAAAA-T-
1 TAAAAAATTA
*
1215 T-AAAATTTA
1 TAAAAAATTA
*
1224 TTAAAAATTA
1 TAAAAAATTA
* *
1234 GAAAAAA-AA
1 TAAAAAATTA
*
1243 TATAAAAATTG
1 TA-AAAAATTA
1254 TAAAAAA
1 TAAAAAA
1261 AATTAGGAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
7 6 0.07
8 8 0.10
9 16 0.19
10 43 0.52
11 8 0.10
12 2 0.02
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:1198 original size:28 final size:27
Alignment explanation
Indices: 1142--1240 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
1132 GCATGTGGTA
* *
1142 AAAAATTATAAAAAA-AAATAATATCAAT
1 AAAAATTATAAAAAATTAA-AAT-TTAAT
1170 AAAAATTAT-AAAAATTATTAAATTTAAT
1 AAAAATTATAAAAAATTA--AAATTTAAT
*
1198 AAAAAATTATAAAAAATTAAAATTTATT
1 -AAAAATTATAAAAAATTAAAATTTAAT
*
1226 AAAAATTAGAAAAAA
1 AAAAATTATAAAAAA
1241 AATATAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 19 0.31
28 22 0.35
29 12 0.19
30 9 0.15
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (27 bp):
AAAAATTATAAAAAATTAAAATTTAAT
Found at i:1211 original size:8 final size:9
Alignment explanation
Indices: 1168--1259 Score: 69
Period size: 9 Copynumber: 9.8 Consensus size: 9
1158 AATAATATCA
1168 ATAAAAATT
1 ATAAAAATT
1177 ATAAAAATT
1 ATAAAAATT
* *
1186 ATTAAATTT
1 ATAAAAATT
1195 AATAAAAAATT
1 -AT-AAAAATT
*
1206 ATAAAAAAT
1 ATAAAAATT
*
1215 -TAAAATTT
1 ATAAAAATT
1223 ATTAAAAATT
1 A-TAAAAATT
* *
1233 AGAAAAAAAAT
1 --ATAAAAATT
1244 ATAAAAATT
1 ATAAAAATT
*
1253 GTAAAAA
1 ATAAAAA
1260 AAATTAGGAA
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
8 6 0.09
9 35 0.55
10 11 0.17
11 11 0.17
12 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1272 original size:20 final size:20
Alignment explanation
Indices: 1225--1263 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1215 TAAAATTTAT
1225 TAAAAATTAG-AAAAAAAATA
1 TAAAAATT-GTAAAAAAAATA
1245 TAAAAATTGTAAAAAAAAT
1 TAAAAATTGTAAAAAAAAT
1264 TAGGAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAAAATTGTAAAAAAAATA
Found at i:1302 original size:19 final size:18
Alignment explanation
Indices: 1278--1323 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1268 AAATTTTTTT
1278 TATAAAAATCATAAAAATA
1 TATAAAAAT-ATAAAAATA
*
1297 TATAAAATATATAGAAATA
1 TATAAAA-ATATAAAAATA
*
1316 TAGAAAAA
1 TATAAAAA
1324 AAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.88
20 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
TATAAAAATATAAAAATA
Done.