Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006191.1 Kokia drynarioides strain JFW-HI SEQ_120760, 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, 774
Length: 1291
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Found at i:620 original size:19 final size:19
Alignment explanation
Indices: 592--646 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
582 GAAGGAATTA
* *
592 AAAATATCAAACATTGGTC
1 AAAATGTCAAACATTAGTC
611 AAAATGTCAAACATTAGTC
1 AAAATGTCAAACATTAGTC
*
630 AAAGATGGCAAACATTA
1 AAA-ATGTCAAACATTA
647 AACAATGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.24
Consensus pattern (19 bp):
AAAATGTCAAACATTAGTC
Found at i:1025 original size:8 final size:8
Alignment explanation
Indices: 1014--1156 Score: 105
Period size: 8 Copynumber: 17.0 Consensus size: 8
1004 CGACCTCTCC
1014 TTTTCTTT
1 TTTTCTTT
1022 TTTTCCATTT
1 TTTT-C-TTT
1032 CTTGTT-TTT
1 -TT-TTCTTT
*
1041 TTTTCTCT
1 TTTTCTTT
*
1049 TTTTCTCT
1 TTTTCTTT
1057 TTTTC-TT
1 TTTTCTTT
1064 TTTTC--T
1 TTTTCTTT
**
1070 TTTTCCGT
1 TTTTCTTT
*
1078 TTTCCTTAT
1 TTTTCTT-T
1087 TTCTTCTTTCT
1 TT-TTC-TT-T
1098 TTTTCTTTT
1 TTTTC-TTT
1107 TTTTCTTT
1 TTTTCTTT
*
1115 TTCTTTTTT
1 TT-TTCTTT
1124 TTTTCTTT
1 TTTTCTTT
1132 TTTTCTTT
1 TTTTCTTT
1140 TTTTCTTT
1 TTTTCTTT
1148 TCTTTCTTT
1 T-TTTCTTT
1157 CTCTTTTTTT
Statistics
Matches: 114, Mismatches: 9, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
6 6 0.05
7 8 0.07
8 53 0.46
9 27 0.24
10 11 0.10
11 7 0.06
12 2 0.02
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1049 original size:15 final size:14
Alignment explanation
Indices: 1031--1167 Score: 90
Period size: 13 Copynumber: 9.7 Consensus size: 14
1021 TTTTTCCATT
1031 TCTTGTTTTTTTTTC
1 TCTT-TTTTTTTTTC
1046 TCTTTTTCTCTTTTTC
1 TCTTTTT-T-TTTTTC
*
1062 T-TTTTTCTTTTTC
1 TCTTTTTTTTTTTC
* *
1075 -CGTTTTCCTTATTTC
1 TC-TTTT-TTTTTTTC
* *
1090 T-TCTTTCTTTTTC
1 TCTTTTTTTTTTTC
1103 T-TTTTTTTCTTTT-
1 TCTTTTTTT-TTTTC
1116 TC-TTTTTTTTTTC
1 TCTTTTTTTTTTTC
*
1129 T-TTTTTTCTTTTTT
1 TCTTTTTT-TTTTTC
*
1143 TCTTTTCTTTCTTTC
1 TCTTTT-TTTTTTTC
1158 TCTTTTTTTT
1 TCTTTTTTTT
1168 CACCGAATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.04
13 30 0.32
14 23 0.24
15 29 0.31
16 9 0.09
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (14 bp):
TCTTTTTTTTTTTC
Found at i:1053 original size:21 final size:20
Alignment explanation
Indices: 1029--1167 Score: 115
Period size: 21 Copynumber: 6.7 Consensus size: 20
1019 TTTTTTTCCA
1029 TTTCTTGTTTTTTTTTCTCTT
1 TTTCTT-TTTTTTTTTCTCTT
1050 TTTCTCTTTTTCTTTTT-TCTT
1 TTTCT-TTTTT-TTTTTCTCTT
* * *
1071 TTTCCGTTTTCCTTATTTCT-TC
1 TTT-C-TTTT-TTTTTTTCTCTT
*
1093 TTTCTTTTTCTTTTTTTTCTT
1 TTTCTTTTT-TTTTTTCTCTT
*
1114 TTTC-TTTTTTTTTTCTTTT
1 TTTCTTTTTTTTTTTCTCTT
1133 TTTCTTTTTTTCTTTTCT-TT
1 TTTCTTTTTTT-TTTTCTCTT
1153 CTTTCTCTTTTTTTT
1 -TTTCT-TTTTTTTT
1168 CACCGAATTT
Statistics
Matches: 97, Mismatches: 9, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
19 13 0.13
20 22 0.23
21 35 0.36
22 24 0.25
23 3 0.03
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTTTTTTTCTCTT
Found at i:1107 original size:1 final size:1
Alignment explanation
Indices: 1097--1167 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
1087 TTCTTCTTTC
* * * * * * * * * *
1097 TTTTTCTTTTTTTTCTTTTTCTTTTTTTTTTCTTTTTTTCTTTTTTTCTTTTCTTTCTTTCTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1162 TTTTTT
1 TTTTTT
1168 CACCGAATTT
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:1154 original size:42 final size:41
Alignment explanation
Indices: 1014--1167 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 41
1004 CGACCTCTCC
** * *
1014 TTTTCTTTTTTTCCATTTCTTGTTTTTTTTTCTCTTTTTCTCT
1 TTTTCTTTTTTTCTTTTTCGT-TTTTTTTTTCTTTTTTTCT-T
* *
1057 TTTTC-TTTTTTCTTTTTCCGTTTTCCTTATTTC-TTCTTTC-T
1 TTTTCTTTTTTTCTTTTT-CGTTTT--TTTTTTCTTTTTTTCTT
1098 TTTTCTTTTTTTTCTTTTTC-TTTTTTTTTTCTTTTTTTCTTT
1 TTTTC-TTTTTTTCTTTTTCGTTTTTTTTTTCTTTTTTTC-TT
*
1140 TTTTCTTTTCTTTCTTTCTC-TTTTTTTT
1 TTTTCTTTT-TTTCTTTTTCGTTTTTTTT
1168 CACCGAATTT
Statistics
Matches: 93, Mismatches: 9, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
39 6 0.06
40 6 0.06
41 14 0.15
42 37 0.40
43 24 0.26
44 6 0.06
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (41 bp):
TTTTCTTTTTTTCTTTTTCGTTTTTTTTTTCTTTTTTTCTT
Found at i:1168 original size:15 final size:15
Alignment explanation
Indices: 1014--1168 Score: 107
Period size: 15 Copynumber: 10.9 Consensus size: 15
1004 CGACCTCTCC
*
1014 TTTTC-TTTTTTTCC
1 TTTTCTTTTTTTTCT
* *
1028 ATTTC-TTGTTTT-T
1 TTTTCTTTTTTTTCT
*
1041 TTTTCTCTTTTTCTCT
1 TTTTCT-TTTTTTTCT
1057 TTTTC--TTTTTTCT
1 TTTTCTTTTTTTTCT
** *
1070 TTTTC-CGTTTTCCT
1 TTTTCTTTTTTTTCT
*
1084 TATTTC--TTCTTTCT
1 T-TTTCTTTTTTTTCT
1098 TTTTCTTTTTTTTCT
1 TTTTCTTTTTTTTCT
1113 TTTTCTTTTTTTT-T
1 TTTTCTTTTTTTTCT
* *
1127 TCTT-TTTTTCTT-T
1 TTTTCTTTTTTTTCT
*
1140 TTTTCTTTTCTTTCT
1 TTTTCTTTTTTTTCT
*
1155 TTCTCTTTTTTTTC
1 TTTTCTTTTTTTTC
1169 ACCGAATTTG
Statistics
Matches: 112, Mismatches: 20, Indels: 17
0.75 0.13 0.11
Matches are distributed among these distances:
13 31 0.28
14 33 0.29
15 42 0.38
16 6 0.05
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Done.