Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005201.1 Kokia drynarioides strain JFW-HI SEQ_119066, 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: 2603
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1287 original size:59 final size:59
Alignment explanation
Indices: 1090--1423 Score: 335
Period size: 58 Copynumber: 5.7 Consensus size: 59
1080 TATCGCCCCT
* * * * *
1090 GAAC-TTCACAAAATTACCATTTTACCCTC-AGATTTCC--AAAATCTAATTTTT-AACTC
1 GAACTTTCCCAAAATTACCATTTTACCCCCGA-ATGTCCAAAAAATC-CATTTTTGACCTC
* * * * * * * *
1146 TGAATTTTCCCAAAATTATCATTTTATCCACGGATGTCCCAAAATTTCATTTTTGACC-C
1 -GAACTTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTC
* *
1205 TAAAC-TTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGATCTC
1 -GAACTTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTC
* * * * *
1264 GAATTTTCCTAAAATTACCATTTTACCCCCAAATTTCC--AAAATCCCATTTTTGACCCC
1 GAACTTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAAT-CCATTTTTGACCTC
* * *
1322 AAACTTTCCCAAAATTACCATTTTATCCCCGAATGTCCAAAAATTCCATTTTTGACCTC
1 GAACTTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTC
* *
1381 GAACTTTCCCAAAATTACTATTTTACCCCCGAACGTCCAAAAA
1 GAACTTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAA
1424 TTATTGATCC
Statistics
Matches: 227, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
57 8 0.04
58 116 0.51
59 93 0.41
60 10 0.04
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
GAACTTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTC
Found at i:1420 original size:117 final size:116
Alignment explanation
Indices: 1091--1422 Score: 386
Period size: 117 Copynumber: 2.9 Consensus size: 116
1081 ATCGCCCCTG
* * * * * *
1091 AACTTCACAAAATTACCATTTTACCCTC-AGATTTCC--AAAATCTAATTTTT-AACTCTGAATT
1 AACTTCCCAAAATTACCATTTTACCCCCGA-ATGTCCAAAAAATC-CATTTTTGACCTC-GAACT
* * * ** *
1152 TTCCCAAAATTA-TCATTTTATCCACGGATGTCCCAAAATTTCATTTTTGACCCTA
63 TTCCCAAAATTACT-ATTTTACCCCCGAATGT-CCAAAATCCCATTTTTGACCCCA
* *
1207 AACTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGATCTCGAATTTTC
1 AACTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTCGAACTTTC
* * * *
1272 CTAAAATTACCATTTTACCCCCAAATTTCCAAAATCCCATTTTTGACCCCA
66 CCAAAATTACTATTTTACCCCCGAATGTCCAAAATCCCATTTTTGACCCCA
* *
1323 AACTTTCCCAAAATTACCATTTTATCCCCGAATGTCCAAAAATTCCATTTTTGACCTCGAACTTT
1 AAC-TTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTCGAACTTT
*
1388 CCCAAAATTACTATTTTACCCCCGAACGTCCAAAA
65 CCCAAAATTACTATTTTACCCCCGAATGTCCAAAA
1423 ATTATTGATC
Statistics
Matches: 186, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
116 54 0.29
117 122 0.66
118 10 0.05
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (116 bp):
AACTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGACCTCGAACTTTC
CCAAAATTACTATTTTACCCCCGAATGTCCAAAATCCCATTTTTGACCCCA
Found at i:1424 original size:59 final size:59
Alignment explanation
Indices: 1151--1425 Score: 349
Period size: 58 Copynumber: 4.7 Consensus size: 59
1141 AACTCTGAAT
* * * * * *
1151 TTTCCCAAAATTATCATTTTATCCACGGATGTCCCAAAATTTCATTTTTGACC-CTAAAC
1 TTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTC-AAAC
* * * *
1210 -TTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAAATCCATTTTTGATCTCGAAT
1 TTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTCAAAC
* * * * *
1268 TTTCCTAAAATTACCATTTTACCCCCAAATTTCC-AAAATCCCATTTTTGACCCCAAAC
1 TTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTCAAAC
* *
1326 TTTCCCAAAATTACCATTTTATCCCCGAATGTCCAAAAATTCCATTTTTGACCTCGAAC
1 TTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTCAAAC
* *
1385 TTTCCCAAAATTACTATTTTACCCCCGAACGTCCAAAAATT
1 TTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATT
1426 ATTGATCCAA
Statistics
Matches: 184, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
58 94 0.51
59 90 0.49
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (59 bp):
TTTCCCAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCATTTTTGACCTCAAAC
Found at i:1425 original size:29 final size:28
Alignment explanation
Indices: 1215--1426 Score: 108
Period size: 29 Copynumber: 7.2 Consensus size: 28
1205 TAAACTTCCC
*
1215 AAAATTACCATTTTACCCCCGAATGTCCA
1 AAAATTACCATTTTA-CCCCGAACGTCCA
* * * ** *
1244 AAAAAT-CCATTTTTGATCTCGAATTTTCCT
1 AAAATTACCA-TTTT-ACCCCGAA-CGTCCA
* **
1274 AAAATTACCATTTTACCCCCAAATTTCC-
1 AAAATTACCATTTTA-CCCCGAACGTCCA
* * * *
1302 AAAA-TCCCATTTTTGACCCCAAACTTTCCC
1 AAAATTACCA-TTTT-ACCCCGAAC-GTCCA
*
1332 AAAATTACCATTTTATCCCCGAATGTCCA
1 AAAATTACCATTTTA-CCCCGAACGTCCA
* * *
1361 AAAATT-CCATTTTTGACCTCGAACTTTCCC
1 AAAATTACCA-TTTT-ACCCCGAAC-GTCCA
*
1391 AAAATTACTATTTTACCCCCGAACGTCCA
1 AAAATTACCATTTTA-CCCCGAACGTCCA
1420 AAAATTA
1 AAAATTA
1427 TTGATCCAAT
Statistics
Matches: 143, Mismatches: 24, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.03
28 21 0.15
29 56 0.39
30 53 0.37
31 9 0.06
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCGAACGTCCA
Done.