Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001352.1 Kokia drynarioides strain JFW-HI SEQ_112801, 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, 934
Length: 1557
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Found at i:234 original size:30 final size:29
Alignment explanation
Indices: 156--332 Score: 121
Period size: 30 Copynumber: 6.0 Consensus size: 29
146 TAGGAGGTTC
** * *
156 GGGGTAAAATGGTAATTTTTAAAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGTTTG
*
185 GAGGTCAAAAAT-G-AGATTTTTGGAAGTTTG
1 GGGGT--AAAATGGTA-ATTTTTGGAAGTTTG
* *
215 GGGGTAAAAATGGTAATTTTGGGAAGGTTCG
1 GGGGT-AAAATGGTAATTTTTGGAA-GTTTG
246 GGGGTAAAATGGTAA-TTTTGTGAAGGTTT-
1 GGGGTAAAATGGTAATTTTTG-GAA-GTTTG
* * * *
275 AGGGTCAAAAATGG-GATTTTTAGAAGTTCG
1 GGGGT--AAAATGGTAATTTTTGGAAGTTTG
* *
305 GGGGTAAAATGGTAATTTTGGGCAGTTT
1 GGGGTAAAATGGTAATTTTTGGAAGTTT
333 AGGGACCTCC
Statistics
Matches: 116, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
28 7 0.06
29 32 0.28
30 51 0.44
31 26 0.22
ACGTcount: A:0.31, C:0.03, G:0.33, T:0.33
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTG
Found at i:244 original size:60 final size:58
Alignment explanation
Indices: 126--245 Score: 168
Period size: 58 Copynumber: 2.0 Consensus size: 58
116 TTGGATGTCC
*
126 CGAGGTCAAAAATGAGATTTTAGGAGGTTCGGGGTAAAATGGTAATTTTTAAAAGGTT
1 CGAGGTCAAAAATGAGATTTTAGGAGGTTCGGGGTAAAATGGTAATTTTGAAAAGGTT
* * * **
184 CGAGGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGGTAATTTTGGGAAGGTT
1 CGAGGTCAAAAATGAGATTTTAGG-AGGTTCGGGGT-AAAATGGTAATTTTGAAAAGGTT
244 CG
1 CG
246 GGGGTAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 23 0.43
59 9 0.17
60 22 0.41
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.31
Consensus pattern (58 bp):
CGAGGTCAAAAATGAGATTTTAGGAGGTTCGGGGTAAAATGGTAATTTTGAAAAGGTT
Found at i:262 original size:90 final size:87
Alignment explanation
Indices: 142--326 Score: 257
Period size: 90 Copynumber: 2.1 Consensus size: 87
132 CAAAAATGAG
*
142 ATTTTAGGAGGTTCGGGGTAAAATGGTAATTTT-TAAAAGGTTCGA-GGTCAAAAATGAGATTTT
1 ATTTTGGGAGGTTCGGGGTAAAATGGTAATTTTGT-AAAGGTT-GAGGGTCAAAAATGAGATTTT
* *
205 TGGAAGTTTGGGGGTAAAAATGGTA
64 TAGAAGTTCGGGGGT-AAAATGGTA
* * *
230 ATTTTGGGAAGGTTCGGGGGTAAAATGGTAATTTTGTGAAGGTTTAGGGTCAAAAATGGGATTTT
1 ATTTTGGG-AGGTTC-GGGGTAAAATGGTAATTTTGTAAAGGTTGAGGGTCAAAAATGAGATTTT
295 TAGAAGTTCGGGGGTAAAATGGTA
64 TAGAAGTTCGGGGGTAAAATGGTA
319 ATTTTGGG
1 ATTTTGGG
327 CAGTTTAGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
88 7 0.08
89 24 0.28
90 55 0.63
91 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (87 bp):
ATTTTGGGAGGTTCGGGGTAAAATGGTAATTTTGTAAAGGTTGAGGGTCAAAAATGAGATTTTTA
GAAGTTCGGGGGTAAAATGGTA
Found at i:265 original size:59 final size:58
Alignment explanation
Indices: 202--325 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 58
192 AAAATGAGAT
* *
202 TTTTGGAA-GTTTGGGGGT-AAAAATGGTAATTTTGGGAAGGTTCGGGGGTAAAATGGTAA
1 TTTTGGAAGGTTT-AGGGTCAAAAATGG-AATTTTGAGAA-GTTCGGGGGTAAAATGGTAA
* *
261 TTTTGTGAAGGTTTAGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAATGGTAA
1 TTTTG-GAAGGTTTAGGGTCAAAAATGGAATTTTGAGAAGTTCGGGGGTAAAATGGTAA
320 TTTTGG
1 TTTTGG
326 GCAGTTTAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
58 1 0.02
59 30 0.52
60 15 0.26
61 12 0.21
ACGTcount: A:0.28, C:0.02, G:0.35, T:0.35
Consensus pattern (58 bp):
TTTTGGAAGGTTTAGGGTCAAAAATGGAATTTTGAGAAGTTCGGGGGTAAAATGGTAA
Found at i:912 original size:44 final size:44
Alignment explanation
Indices: 849--947 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
839 AAACATTTCC
* *
849 TTCGCCCTTTTTTAAAAAAAACCCAAAATCCTCTCCAAAATTCT
1 TTCGCCCCTTTTTAAAAAAAACCCAAAATCCTCTCCAAAATCCT
893 TTCGCCCCTTTTTAAAAAAAACCCAAAATCCTCTCCAAAATCCT
1 TTCGCCCCTTTTTAAAAAAAACCCAAAATCCTCTCCAAAATCCT
*
937 CTCGCCCCTTT
1 TTCGCCCCTTT
948 CCGGCTGGCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.32, C:0.34, G:0.03, T:0.30
Consensus pattern (44 bp):
TTCGCCCCTTTTTAAAAAAAACCCAAAATCCTCTCCAAAATCCT
Found at i:932 original size:12 final size:12
Alignment explanation
Indices: 915--939 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
905 TAAAAAAAAC
915 CCAAAATCCTCT
1 CCAAAATCCTCT
927 CCAAAATCCTCT
1 CCAAAATCCTCT
939 C
1 C
940 GCCCCTTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (12 bp):
CCAAAATCCTCT
Found at i:1485 original size:21 final size:21
Alignment explanation
Indices: 1461--1516 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1451 TTAAAACATT
1461 TATTATTAATGCCTTTATTAA
1 TATTATTAATGCCTTTATTAA
* ***
1482 TATTAATAATAATTTTATTAA
1 TATTATTAATGCCTTTATTAA
1503 TATCTATTAATGCC
1 TAT-TATTAATGCC
1517 AATATTTATT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.50
Consensus pattern (21 bp):
TATTATTAATGCCTTTATTAA
Done.