Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008424.1 Kokia drynarioides strain JFW-HI SEQ_123095, 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: 3986
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Found at i:92 original size:49 final size:49
Alignment explanation
Indices: 1--216 Score: 160
Period size: 49 Copynumber: 4.4 Consensus size: 49
* * *
1 GACTTAAACCTTTCCC-TCTATGTCTTCGTG-GTAC-TGGATTCGCCGTTGC
1 GACTTAAATCTTTCCCTTC-ATGTCTTC-TGATTACAAGG-TTCGCCGTTGC
* **
50 GGCTTAAATCTTTCCCTTCATGTC-TCTGATATACAAGGTTCGCTATTGC
1 GACTTAAATCTTTCCCTTCATGTCTTCTGAT-TACAAGGTTCGCCGTTGC
* * * * *
99 GACTTAAATCTTTCCC-TCTATATCTTCGTGGTT-C-TGCATTCACCGTTGC
1 GACTTAAATCTTTCCCTTC-ATGTCTTC-TGATTACAAG-GTTCGCCGTTGC
* * * *
148 GGCTTAAATCTTTCCCTTCATG-CTTTTGAGGTACAAGGTTTGCCGTTGC
1 GACTTAAATCTTTCCCTTCATGTCTTCTGA-TTACAAGGTTCGCCGTTGC
*
197 GACTTAAACCTTTCCCTTCA
1 GACTTAAATCTTTCCCTTCA
217 AATCGTCATT
Statistics
Matches: 130, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
47 4 0.03
48 9 0.07
49 104 0.80
50 10 0.08
51 3 0.02
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (49 bp):
GACTTAAATCTTTCCCTTCATGTCTTCTGATTACAAGGTTCGCCGTTGC
Found at i:183 original size:98 final size:98
Alignment explanation
Indices: 1--213 Score: 311
Period size: 98 Copynumber: 2.2 Consensus size: 98
* * *
1 GACTTAAACCTTTCCCTCTATGTCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCTATATCTTCGTGGTACTGCATTCACCGTTGCGGCTTAAATCTTTCCC
* *
66 TTCATGTCTCTGATATACAAGGTTCGCTATTGC
66 TTCATGTCTCTGAGATACAAGGTTCGCCATTGC
* *
99 GACTTAAATCTTTCCCTCTATATCTTCGTGGTTCTGCATTCACCGTTGCGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCTATATCTTCGTGGTACTGCATTCACCGTTGCGGCTTAAATCTTTCCC
* * * *
164 TTCATG-CTTTTGAGGTACAAGGTTTGCCGTTGC
66 TTCATGTC-TCTGAGATACAAGGTTCGCCATTGC
197 GACTTAAACCTTTCCCT
1 GACTTAAACCTTTCCCT
214 TCAAATCGTC
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
97 1 0.01
98 101 0.99
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.38
Consensus pattern (98 bp):
GACTTAAACCTTTCCCTCTATATCTTCGTGGTACTGCATTCACCGTTGCGGCTTAAATCTTTCCC
TTCATGTCTCTGAGATACAAGGTTCGCCATTGC
Found at i:1178 original size:6 final size:6
Alignment explanation
Indices: 1169--1272 Score: 75
Period size: 6 Copynumber: 16.3 Consensus size: 6
1159 CGACCTCTCC
* * * * * *
1169 TTTTCT TTTTCC ATTTC- TTCTAT TTTTGT TTTTCT TTTTGT TTTCCTCTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTT--TC-T
*
1219 TTTTCT TTTTCT TTTTCT TTTTCATT TTCTTCT TCTTCT TTTTCTT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTC--T TT-TTCT TTTTCT TTTTC-T TTTTCT
1271 TT
1 TT
1273 ATTCATTGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
5 2 0.03
6 55 0.71
7 10 0.13
8 4 0.05
9 7 0.09
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:1223 original size:21 final size:19
Alignment explanation
Indices: 1197--1272 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 19
1187 TCTATTTTTG
*
1197 TTTTTCTTTTTGTTTTCCTC
1 TTTTTCTTTTTCTTTT-CTC
1217 TTTTTTCTTTTTCTTTT-TC
1 -TTTTTCTTTTTCTTTTCTC
*
1236 TTTTTCATTTTCTTCTTCTTC
1 TTTTTCTTTTTCTT-TTC-TC
1257 TTTTTCTTTTTTCTTT
1 TTTTTC-TTTTTCTTT
1273 ATTCATTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.27
19 4 0.08
21 24 0.50
22 7 0.15
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTCTC
Found at i:1229 original size:27 final size:26
Alignment explanation
Indices: 1169--1272 Score: 102
Period size: 27 Copynumber: 3.8 Consensus size: 26
1159 CGACCTCTCC
* *
1169 TTTTCTTTTTCCATTTCTTCTATTTTTGT
1 TTTTCTTTTT-CTTTTC-TCT-TTTTTCT
*
1198 TTTTCTTTTTGTTTTCCTCTTTTTTCT
1 TTTTCTTTTTCTTTT-CTCTTTTTTCT
1225 TTTTCTTTTTCTTTT-TCATTTTCTTCT
1 TTTTCTTTTTCTTTTCTC-TTTT-TTCT
* *
1252 TCTTCTTTTTCTTTTTTCTTT
1 TTTTCTTTTTCTTTTCTCTTT
1273 ATTCATTGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.03
26 4 0.06
27 41 0.62
28 8 0.12
29 11 0.17
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTCTTTTTCTTTTCTCTTTTTTCT
Found at i:1234 original size:33 final size:33
Alignment explanation
Indices: 1169--1279 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
1159 CGACCTCTCC
* *
1169 TTTTCTTTTTCCAT-TTCTTCTATTTTTGTTTTTCT
1 TTTTCATTTTCC-TCTTCTTC--TTTTTCTTTTTCT
* *
1204 TTTT-GTTTTCCTCTTTTTTCTTTTTCTTTTTCT
1 TTTTCATTTTCCTC-TTCTTCTTTTTCTTTTTCT
*
1237 TTTTCATTTTCTTCTTCTTCTTTTTCTTTTTTCT
1 TTTTCATTTTCCTCTTCTTCTTTTTC-TTTTTCT
1271 TTATTCATT
1 TT-TTCATT
1280 GAATCCGAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
33 28 0.43
34 22 0.34
35 15 0.23
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (33 bp):
TTTTCATTTTCCTCTTCTTCTTTTTCTTTTTCT
Done.