Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000135.1 Kokia drynarioides strain JFW-HI SEQ_110785, 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: 5624
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Found at i:119 original size:26 final size:24
Alignment explanation
Indices: 89--137 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
79 TTAATTTTGT
*
89 AAATGAACTATTTTTTTTTTATTTTA
1 AAATGAAC--TTTTATTTTTATTTTA
*
115 AAATGGACTTTTATTTTTATTTT
1 AAATGAACTTTTATTTTTATTTT
138 TGTTTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
26 7 0.33
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (24 bp):
AAATGAACTTTTATTTTTATTTTA
Found at i:599 original size:100 final size:100
Alignment explanation
Indices: 400--694 Score: 270
Period size: 100 Copynumber: 2.9 Consensus size: 100
390 GGCAACCTCA
* ** * * ** * *
400 AGGAG-ATCAAGATTTGCTTCTATGGCTTTAATTTGCTCCTCTACAGTTTTAGGGGGTATAAGAT
1 AGGAGCAT-AAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAACTGTA-GAGGTATAAGAT
* * * * * *
464 TTGATTTTACAACTTTAATTTGCCCCTCTATGGCTTT
64 TTGCTTCTACAGCTTCAATCTGCCCCTCTACGGCTTT
*
501 A-GAGGCATAAGATTTACTTCTACATCTTCAATTTGCCCCTCTACAACTGTAGAGGTATAAGATT
1 AGGA-GCATAAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAACTGTAGAGGTATAAGATT
*
565 TGCTTCTATAGCTTCAATCTGCCCCTCTACGGCTTT
65 TGCTTCTACAGCTTCAATCTGCCCCTCTACGGCTTT
* * * * * * * ****
601 AGGAGTATAAGATTTTCTTCTATAGCTTTAATTTGCCCCTTTACAACTTTAGGGGTAATTTTTTT
1 AGGAGCATAAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAACTGTAGAGGT-ATAAGATT
* *
666 TGCTTCTGCAGCTTCAATCTGTCCCTCTA
65 TGCTTCTACAGCTTCAATCTGCCCCTCTA
695 AATTTAGGGG
Statistics
Matches: 158, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
100 88 0.56
101 68 0.43
102 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (100 bp):
AGGAGCATAAGATTTACTTCTACAGCTTCAATTTGCCCCTCTACAACTGTAGAGGTATAAGATTT
GCTTCTACAGCTTCAATCTGCCCCTCTACGGCTTT
Found at i:651 original size:50 final size:50
Alignment explanation
Indices: 400--653 Score: 244
Period size: 50 Copynumber: 5.1 Consensus size: 50
390 GGCAACCTCA
* * *
400 AGGAG-ATCAAGATTTGCTTCTATGGCTTTAATTTGCTCCTCTACAGTTTT
1 AGGAGTAT-AAGATTTGCTTCTATAGCTTTAATTTGCCCCTCTACAGCTTT
* * * * * **
450 AGGGGGTATAAGATTTGATTTTACAACTTTAATTTGCCCCTCTATGGCTTT
1 A-GGAGTATAAGATTTGCTTCTATAGCTTTAATTTGCCCCTCTACAGCTTT
* * * * * * *
501 A-GAGGCATAAGATTTACTTCTACATCTTCAATTTGCCCCTCTACAACTGT
1 AGGA-GTATAAGATTTGCTTCTATAGCTTTAATTTGCCCCTCTACAGCTTT
* * *
551 A-GAGGTATAAGATTTGCTTCTATAGCTTCAATCTGCCCCTCTACGGCTTT
1 AGGA-GTATAAGATTTGCTTCTATAGCTTTAATTTGCCCCTCTACAGCTTT
* * *
601 AGGAGTATAAGATTTTCTTCTATAGCTTTAATTTGCCCCTTTACAACTTT
1 AGGAGTATAAGATTTGCTTCTATAGCTTTAATTTGCCCCTCTACAGCTTT
651 AGG
1 AGG
654 GGTAATTTTT
Statistics
Matches: 165, Mismatches: 35, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
49 1 0.01
50 123 0.75
51 39 0.24
52 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (50 bp):
AGGAGTATAAGATTTGCTTCTATAGCTTTAATTTGCCCCTCTACAGCTTT
Found at i:934 original size:46 final size:46
Alignment explanation
Indices: 676--1145 Score: 451
Period size: 46 Copynumber: 10.1 Consensus size: 46
666 TGCTTCTGCA
* * *
676 GCTTCAATCTGTCCCTCTAAATTTAGGGGTATAAG-TTGGATGTAGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATG--GTG
* * * *
723 GCTTGAATCTGCCCCTTTGGATTTAGAGTTATAAGATTGGATGTGGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGA--TGGTG
* * * *
771 GTTTCAATCTGCCCTTTTAGATTTAGGAGTATAAGATTGGATATGATG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGG--ATGGTG
* * * * * *
819 ACTTTAATCTGTCCTTTTGGATTTAAGGGTATAAGATTGGATGTGGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGA--TGGTG
* * *
867 GCTCCAATCTGCCCCTCTAGATTTAGGGGTATAAGATTCGATGGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGGTG
* * *
913 ACTTCAATTTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGGCG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGGTG
* * *
959 GCTTCAATCTACCCCTTTAGATTTAGGGGTATAAGATTAGATGTTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGGTG
* ** * ** *
1005 GATTCAAT-TTTCCCTTCTGGATTTATCGATATAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTT-TAGATTTAGGGGTATAAGATTGGATGGTG
* * * * *
1051 ACTTCAATCTGCCTCTTTGGATTTAGGGGTATAAGAACT-AATGGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAG-ATTGGATGGTG
* * * *
1097 GCTTCAATCTACCCCTCTGGATTTAGGGGTATAAGATTGGATCGTG
1 GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGGTG
1143 GCT
1 GCT
1146 ACGTAAATTC
Statistics
Matches: 342, Mismatches: 70, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
45 8 0.02
46 182 0.53
47 35 0.10
48 114 0.33
50 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (46 bp):
GCTTCAATCTGCCCCTTTAGATTTAGGGGTATAAGATTGGATGGTG
Found at i:1356 original size:99 final size:99
Alignment explanation
Indices: 1148--1645 Score: 402
Period size: 99 Copynumber: 5.0 Consensus size: 99
1138 TCGTGGCTAC
* * * * *
1148 GTAAATTCACTCCATTCCACTGCAACTTCAGGGAGATTGAGATCCGCTACTATATTTTTAATCGG
1 GTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGCTACT-T-GTTTTAATCCG
* * *
1213 CTTCACTGCAACTTCAAGAAGATAGGATTTGGTGTG
64 ATTCACTGTAACTTCAAGGAGATAGGATTTGGTGTG
* *
1249 GTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGA-AGTTCGTTACTTGTTTTAATCCGA
1 GTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGA-TTCGCTACTTGTTTTAATCCGA
* * * *
1313 TCCACTGTAAGTTCAAGGATATAGGATTTGAG-GTT
65 TTCACTGTAACTTCAAGGAGATAGGATTTG-GTGTG
** * * * * * *
1348 GTGGCTTCAATGCATTCCACTGCAACTT-TAGTAGATATTGAGATTTGCTACTTGTTTTACTCC-
1 GTAACTTCACTCCATTCCACTGCAACTTCAAG--GAGATTGAGATTCGCTACTTGTTTTAATCCG
*
1411 ACTTCACT-TCAACTT-TAGGAAGATAGGATTTGGTGTG
64 A-TTCACTGT-AACTTCAAGG-AGATAGGATTTGGTGTG
* * * * * * * * * *
1448 GTAACTTCGCTCTATTCTATTGTAACTTC-AGCGAGATCGAGGTCCGTTACTTGTTTTAATTCGA
1 GTAACTTCACTCCATTCCACTGCAACTTCAAG-GAGATTGAGATTCGCTACTTGTTTTAATCCGA
* * * *
1512 TTTACTGTAACTTCAGGGATATAGGATTTGAG-GTT
65 TTCACTGTAACTTCAAGGAGATAGGATTTG-GTGTG
** * * * *
1547 GTGGCTTTACTCCATTCCACTGCAACTTCAATAGAGATTGAGATTTGCTACTTGTTTTAATCCGC
1 GTAACTTCACTCCATTCCACTGCAACTTCAA-GGAGATTGAGATTCGCTACTTGTTTTAATCCGA
* * *
1612 TTCACTGCAACTTC-GGGAAGGTAGGATTTGGTGT
65 TTCACTGTAACTTCAAGG-AGATAGGATTTGGTGT
1646 TTCACTGGTC
Statistics
Matches: 307, Mismatches: 72, Indels: 37
0.74 0.17 0.09
Matches are distributed among these distances:
98 2 0.01
99 135 0.44
100 125 0.41
101 45 0.15
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (99 bp):
GTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTCGCTACTTGTTTTAATCCGAT
TCACTGTAACTTCAAGGAGATAGGATTTGGTGTG
Found at i:1553 original size:199 final size:199
Alignment explanation
Indices: 1153--1645 Score: 666
Period size: 199 Copynumber: 2.5 Consensus size: 199
1143 GCTACGTAAA
* * ** * *
1153 TTCACTCCATTCCACTGCAACTTCAG-GGAGATTGAGATCCGCTACTATATTTTTAATCGGCTTC
1 TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACT-T-GTTTTAATCCGCTTC
*
1217 ACTGCAACTTCAAGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGG
64 ACTGCAACTTCAGGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGG
* * *
1282 AGATTGAAGTTCGTTACTTGTTTTAATCCGATCCACTGTAAGTTCAAGGATATAGGATTTGAGGT
129 AGATCGAAGTCCGTTACTTGTTTTAATCCGATCCACTGTAACTTCAAGGATATAGGATTTGAGGT
1347 TGTGGC
194 TGTGGC
* * * * *
1353 TTCAATGCATTCCACTGCAACTTTAGTAGATATTGAGATTTGCTACTTGTTTTACTCCACTTCAC
1 TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
* * * * * *
1418 TTCAACTTTAGGAAGATAGGATTTGGTGTGGTAACTTCGCTCTATTCTATTGTAACTTC-AGCGA
66 TGCAACTTCAGGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAG-GA
* * ** *
1482 GATCGAGGTCCGTTACTTGTTTTAATTCGATTTACTGTAACTTCAGGGATATAGGATTTGAGGTT
130 GATCGAAGTCCGTTACTTGTTTTAATCCGATCCACTGTAACTTCAAGGATATAGGATTTGAGGTT
1547 GTGGC
195 GTGGC
* * *
1552 TTTACTCCATTCCACTGCAACTTCAATAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
1 TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
* *
1617 TGCAACTTCGGGAAGGTAGGATTTGGTGT
66 TGCAACTTCAGGAAGATAGGATTTGGTGT
1646 TTCACTGGTC
Statistics
Matches: 253, Mismatches: 38, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
198 2 0.01
199 211 0.83
200 24 0.09
201 16 0.06
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (199 bp):
TTCAATCCATTCCACTGCAACTTCAGTAGAGATTGAGATTTGCTACTTGTTTTAATCCGCTTCAC
TGCAACTTCAGGAAGATAGGATTTGGTGTGGTAACTTCACTCCATTCCACTGTAACTTCAAGGAG
ATCGAAGTCCGTTACTTGTTTTAATCCGATCCACTGTAACTTCAAGGATATAGGATTTGAGGTTG
TGGC
Found at i:2450 original size:26 final size:26
Alignment explanation
Indices: 2412--2462 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
2402 CAACCTCTCT
*
2412 TTTTCCTTTTCCTTTTTCTCTTTTTTC
1 TTTTCCTTTTCC-TTTTCCCTTTTTTC
2439 TTTT-CTTTTCCTTTTCCCTTTTTT
1 TTTTCCTTTTCCTTTTCCCTTTTTT
2463 TTGGGGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 7 0.30
27 4 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTCCTTTTCCTTTTCCCTTTTTTC
Found at i:2463 original size:26 final size:27
Alignment explanation
Indices: 2412--2462 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
2402 CAACCTCTCT
*
2412 TTTTCCTTTTCCTTTTTCTCTTTTTTC
1 TTTTCCTTTTCCTTTTCCTCTTTTTTC
2439 TTTT-CTTTTCCTTTTCC-CTTTTTT
1 TTTTCCTTTTCCTTTTCCTCTTTTTT
2463 TTGGGGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTTCCTTTTCCTTTTCCTCTTTTTTC
Done.