Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010283.1 Kokia drynarioides strain JFW-HI SEQ_125132, 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: 15982
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:132 original size:20 final size:20
Alignment explanation
Indices: 104--170 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
94 TCATGTCAGT
*
104 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
124 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
* *
144 AAATTATTTAAAAATTTTTA
1 AAATTATTTTAAAATTATTA
164 AAATTAT
1 AAATTAT
171 GATCACCATC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.17
19 1 0.03
20 22 0.55
21 2 0.05
22 8 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:1148 original size:38 final size:38
Alignment explanation
Indices: 1082--1181 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
1072 GATGATGATT
* *
1082 ATAATTTTAAATAATTGTAATTATTTTATATTTT-AAAA
1 ATAATTTTAAATAATTTTAA-TAATTTATATTTTAAAAA
*
1120 ATATTTTTAAATTAATTTTAATAATTTATATTTTAAAAA
1 ATAATTTTAAA-TAATTTTAATAATTTATATTTTAAAAA
1159 ATAATTTT-AATAATTTTAA-AATT
1 ATAATTTTAAATAATTTTAATAATT
1182 ATTTGTTGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
36 4 0.07
37 9 0.16
38 24 0.43
39 19 0.34
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
ATAATTTTAAATAATTTTAATAATTTATATTTTAAAAA
Found at i:1154 original size:15 final size:14
Alignment explanation
Indices: 1131--1174 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1121 TATTTTTAAA
1131 TTAATTTTAATAAT
1 TTAATTTTAATAAT
*
1145 TTATATTTTAA-AAA
1 TTA-ATTTTAATAAT
*
1159 ATAATTTTAATAAT
1 TTAATTTTAATAAT
1173 TT
1 TT
1175 TAAAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 7 0.29
14 10 0.42
15 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATTTTAATAAT
Found at i:1664 original size:20 final size:21
Alignment explanation
Indices: 1639--1679 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1629 TATGTGACCG
*
1639 ATAAAAAAAA-TCGTAATTGA
1 ATAAAAAAAACTCATAATTGA
1659 ATAAAAAAAACTCATAATTGA
1 ATAAAAAAAACTCATAATTGA
1680 TTGAATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (21 bp):
ATAAAAAAAACTCATAATTGA
Found at i:4343 original size:7 final size:7
Alignment explanation
Indices: 4331--4361 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4321 TTGTTTCATA
4331 CCATTTG
1 CCATTTG
4338 CCATTTG
1 CCATTTG
4345 CCATTTG
1 CCATTTG
4352 CCATTTG
1 CCATTTG
4359 CCA
1 CCA
4362 CCCACAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.32, G:0.13, T:0.39
Consensus pattern (7 bp):
CCATTTG
Found at i:7889 original size:88 final size:88
Alignment explanation
Indices: 7740--7917 Score: 356
Period size: 88 Copynumber: 2.0 Consensus size: 88
7730 TTCACCAAAA
7740 AAATGTATGTTAATTATGAATATAAAAGTAAAATACAAATACTCATTATATTTGGTATTGCATTA
1 AAATGTATGTTAATTATGAATATAAAAGTAAAATACAAATACTCATTATATTTGGTATTGCATTA
7805 TTTTCATTTATGCTTCTTTATTT
66 TTTTCATTTATGCTTCTTTATTT
7828 AAATGTATGTTAATTATGAATATAAAAGTAAAATACAAATACTCATTATATTTGGTATTGCATTA
1 AAATGTATGTTAATTATGAATATAAAAGTAAAATACAAATACTCATTATATTTGGTATTGCATTA
7893 TTTTCATTTATGCTTCTTTATTT
66 TTTTCATTTATGCTTCTTTATTT
7916 AA
1 AA
7918 GACATTGTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (88 bp):
AAATGTATGTTAATTATGAATATAAAAGTAAAATACAAATACTCATTATATTTGGTATTGCATTA
TTTTCATTTATGCTTCTTTATTT
Found at i:10277 original size:76 final size:76
Alignment explanation
Indices: 10151--10303 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
10141 TTTCATATCA
10151 TATAAATAGTTAAATTACATCATCTTAAAGACAGAGAAAATTACTCAACAATCAACCTTGAATTT
1 TATAAATAGTTAAATTACATCATCTTAAAGACAGAGAAAATTACTCAACAATCAACCTTGAATTT
10216 TGATTTTTTTT
66 TGATTTTTTTT
10227 TATAAATAGTTAAATTACATCATCTTAAAGACAGAGAAAATTACTCAACAATCAACCTTGAATTT
1 TATAAATAGTTAAATTACATCATCTTAAAGACAGAGAAAATTACTCAACAATCAACCTTGAATTT
10292 TGATTTTTTTT
66 TGATTTTTTTT
10303 T
1 T
10304 TTTTTAATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.39
Consensus pattern (76 bp):
TATAAATAGTTAAATTACATCATCTTAAAGACAGAGAAAATTACTCAACAATCAACCTTGAATTT
TGATTTTTTTT
Found at i:10884 original size:19 final size:16
Alignment explanation
Indices: 10849--10887 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
10839 TTTTTTTATC
10849 TTTTAAATAAAAAATA
1 TTTTAAATAAAAAATA
*
10865 TTTTAATATAGAAAATA
1 TTTTAA-ATAAAAAATA
10882 TATTTA
1 T-TTTA
10888 CAAAGTCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTTAAATAAAAAATA
Found at i:15785 original size:17 final size:17
Alignment explanation
Indices: 15761--15834 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
15751 TTGGAAATTG
15761 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
15778 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
15795 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
15812 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
15829 AATTTA
1 AATTTA
15835 GAAAAGTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Done.